Merge pull request #1374 from nsoranzo/fix_master

Fix links

cwl-runner/README

@@ -1,9 +1,9 @@
-This an optional companion package to planemo which provides provides
+This an optional companion package to planemo which provides
 an additional entry point under the alias "cwl-runner", which is the
 implementation-agnostic name for the default CWL interpreter installed
 on a host.
 
 This package is based on the CWL reference implementation package of
 the same name, see
-https://github.com/common-workflow-language/cwltool/tree/master/cwl-runner
+https://github.com/common-workflow-language/cwltool/tree/main/cwlref-runner
 for more information.

docs/_writing_clusters.rst

@@ -10,9 +10,9 @@ tool's runtime environment. If the tool you are working on allows configuring
 the number of processes or threads that should be spawned, this variable
 should be used.
 
-For example, the StringTie (tool available `here
-<https://github.com/galaxyproject/tools-iuc/blob/master/tools/stringtie/stringtie.xml>`__)
-binary ``stringtie`` can take an argument ``-p`` that allows specification
+For example, for the `StringTie tool
+<https://github.com/galaxyproject/tools-iuc/blob/main/tools/stringtie/stringtie.xml>`__
+the binary ``stringtie`` can take an argument ``-p`` that allows specification
 of the number of threads to be used. The Galaxy tool sets this up as follows
 
 ::
@@ -35,7 +35,7 @@ environment variables in a Galaxy tool's runtime environment that can be used
 to specify the amount of memory that a tool can use overall and per slot,
 respectively. 
 
-For an example see the samtools sort tool (`here <https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/samtools/samtools_sort/samtools_sort.xml>`__) which allows to specify the
+For an example see the `samtools sort tool <https://github.com/galaxyproject/tools-iuc/blob/main/tool_collections/samtools/samtools_sort/samtools_sort.xml>`__ which allows to specify the
 total memory with the -m parameter.
 
 -----------------------------------------------

docs/_writing_collections.rst

@@ -117,9 +117,9 @@ arbitrary collection types an array syntax can also be used (e.g.
 Some example tools which consume paired datasets include:
 
  - `collection_paired_test <https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_paired_test.xml>`__ (minimal test tool in Galaxy test suite)
- - `Bowtie 2 <https://github.com/galaxyproject/tools-devteam/blob/master/tools/bowtie2/bowtie2_wrapper.xml>`__
- - `BWA MEM <https://github.com/galaxyproject/tools-devteam/blob/master/tools/bwa/bwa-mem.xml>`__
- - `Tophat <https://github.com/galaxyproject/tools-devteam/blob/master/tools/tophat2/tophat2_wrapper.xml>`__
+ - `Bowtie 2 <https://github.com/galaxyproject/tools-iuc/blob/main/tools/bowtie2/bowtie2_wrapper.xml>`__
+ - `BWA MEM <https://github.com/galaxyproject/tools-iuc/blob/main/tools/bwa/bwa-mem.xml>`__
+ - `Tophat <https://github.com/galaxyproject/tools-devteam/blob/main/tools/tophat2/tophat2_wrapper.xml>`__
 
 Processing Lists (Reductions)
 -------------------------------
@@ -175,8 +175,8 @@ the idiom:
 Some example tools which consume multiple datasets (including lists) include:
 
  - `multi_data_param <https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_data_param.xml>`__ (small test tool in Galaxy test suite)
- - `cuffmerge tool macros <https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/cufflinks/cuff_macros.xml>`__
- - `unionBedGraphs <https://github.com/galaxyproject/tools-iuc/blob/master/tools/bedtools/unionBedGraphs.xml>`__
+ - `cuffmerge tool macros <https://github.com/galaxyproject/tools-iuc/blob/main/tool_collections/cufflinks/cuff_macros.xml>`__
+ - `unionBedGraphs <https://github.com/galaxyproject/tools-iuc/blob/main/tools/bedtools/unionBedGraphs.xml>`__
 
 Also see the tools-devteam repository `Pull Request #20 <https://github.com/galaxyproject/tools-devteam/pull/20>`__ modifying the cufflinks suite of tools for collection compatible reductions.
 
@@ -215,9 +215,9 @@ Some example tools which utilize ``element_identifier`` include:
 
  - `identifier_multiple <https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/identifier_multiple.xml>`__
  - `identifier_single <https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/identifier_single.xml>`__
- - `vcftools_merge <https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/vcftools/vcftools_merge/vcftools_merge.xml>`__
- - `jbrowse <https://github.com/galaxyproject/tools-iuc/blob/master/tools/jbrowse/jbrowse.xml>`_
- - `kraken-mpa-report <https://github.com/blankenberg/tools-devteam/blob/master/tool_collections/kraken/kraken_report/kraken-mpa-report.xml>`__
+ - `vcftools_merge <https://github.com/galaxyproject/tools-devteam/blob/main/tool_collections/vcftools/vcftools_merge/vcftools_merge.xml>`__
+ - `jbrowse <https://github.com/galaxyproject/tools-iuc/blob/main/tools/jbrowse/jbrowse.xml>`_
+ - `kraken-mpa-report <https://github.com/galaxyproject/tools-iuc/blob/main/tool_collections/kraken/kraken-mpa-report.xml>`__
 
 More on ``data_collection`` parameters
 ----------------------------------------------

docs/_writing_intro.rst

@@ -4,7 +4,7 @@ The Basics
 .. include:: _writing_using_seqtk.rst
 
 For fully featured Seqtk wrappers check out Helena Rasche's
-`wrappers <https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk>`__
+`wrappers <https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk>`__
 on GitHub.
 
 Galaxy tool files are just XML files, so at this point one could

docs/_writing_multiple_outputs.rst

@@ -101,7 +101,7 @@ A common usage of this strategy is to have the primary dataset be an HTML file a
 
 If you want to wrap or create a tool that generates an HTML history item that shows the user links to a number of related output objects (files, images..), you need to know where to write the objects and how to reference them when your tool generates HTML which gets written to the HTML file. Galaxy will not write that HTML for you at present.
 
-The `fastqc wrapper <https://github.com/galaxyproject/tools-devteam/blob/master/tools/fastqc/rgFastQC.xml>`__ is an existing tool example where the Java application generates HTML and image outputs but these need to be massaged to make them Galaxy friendly. In other cases, the application or your wrapper must take care of all the fiddly detailed work of writing valid html to display to the user. In either situation, the ``html`` datatype offers a flexible way to display very complex collections of related outputs inside a single history item or to present a complex html page generated by an application. There are some things you need to take care of for this to work:
+The `FastQC wrapper <https://github.com/galaxyproject/tools-iuc/blob/main/tools/fastqc/rgFastQC.xml>`__ is an existing tool example where the Java application generates HTML and image outputs but these need to be massaged to make them Galaxy friendly. In other cases, the application or your wrapper must take care of all the fiddly detailed work of writing valid html to display to the user. In either situation, the ``html`` datatype offers a flexible way to display very complex collections of related outputs inside a single history item or to present a complex html page generated by an application. There are some things you need to take care of for this to work:
 
 The following example demonstrates declaring an output of type ``html``.
 
@@ -131,7 +131,7 @@ The application must create and write valid html to setup the page ``$html_file`
     <br/>
     <img src="image1.jpg" >
 
-The (now unmaintained) Galaxy Tool Factory includes code to gather all output files and create a page with links and clickable PDF thumbnail images which may be useful as a starting point (e.g. see `rgToolFactory2.py <https://github.com/galaxyproject/tools-iuc/blob/master/tools/tool_factory_2/rgToolFactory2.py#L741>`__.
+The (now unmaintained) Galaxy Tool Factory includes code to gather all output files and create a page with links and clickable PDF thumbnail images which may be useful as a starting point (e.g. see `rgToolFactory2.py <https://github.com/galaxyproject/tools-iuc/blob/main/deprecated/tools/tool_factory_2/rgToolFactory2.py#L742>`__.
 
 ``galaxy.datatypes.text.Html`` (the ``html`` datatype) is a subclass of composite datasets so new subclasses of composite can be used to implement even more specific structured outputs but this requires adding the new definition to Galaxy - whereas Html files require no extension of the core framework. For more information visit `Composite Datatypes <https://docs.galaxyproject.org/en/master/dev/data_types.html#composite-datatypes>`__. 
 

docs/_writing_suites.rst

@@ -41,9 +41,9 @@ to avoid duplication and keep your XML concise.
 Further reading:
 
 - `Macros syntax <https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Reusing_Repeated_Configuration_Elements>`__ on the Galaxy Wiki.
-- `GATK tools <https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2>`__ (example tools making extensive use of macros)
-- `gemini tools <https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini>`__ (example tools making extensive use of macros)
-- `bedtools tools <https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools>`__ (example tools making extensive use of macros)
+- `GATK tools <https://github.com/galaxyproject/tools-iuc/tree/main/deprecated/tools/gatk2>`__ (example tools making extensive use of macros)
+- `gemini tools <https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini>`__ (example tools making extensive use of macros)
+- `bedtools tools <https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools>`__ (example tools making extensive use of macros)
 - Macros implementation details - `Pull Request #129 <https://bitbucket.org/galaxy/galaxy-central/pull-request/129/implement-macro-engine-to-reduce-tool/diff>`__ and `Pull Request #140 <https://bitbucket.org/galaxy/galaxy-central/pull-request/140/improvements-to-tool-xml-macroing-system/diff>`__
 
 .. _macros: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Reusing_Repeated_Configuration_Elements

docs/galaxy_changelog.html

@@ -146,7 +146,7 @@
 simple command-line tools - but complex tools with many repeats, conditional,
 and nesting could potentially benefit from this.
 
-For instance, the [JBrowse](https://github.com/galaxyproject/tools-iuc/blob/master/tools/jbrowse/jbrowse.xml)
+For instance, the [JBrowse](https://github.com/galaxyproject/tools-iuc/blob/main/tools/jbrowse/jbrowse.xml)
 tool generates a complex JSON data structure using a `configfile` inside the
 XML. This is a much more portable way to deal with that.
 
@@ -270,4 +270,4 @@
       var slideshow = remark.create();
     </script>
   </body>
-</html>
+</html>

docs/galaxy_changelog.md

@@ -132,7 +132,7 @@ JSON structure corresponding to the tools inputs. Of limitted utility for
 simple command-line tools - but complex tools with many repeats, conditional,
 and nesting could potentially benefit from this.
 
-For instance, the [JBrowse](https://github.com/galaxyproject/tools-iuc/blob/master/tools/jbrowse/jbrowse.xml)
+For instance, the [JBrowse](https://github.com/galaxyproject/tools-iuc/blob/main/tools/jbrowse/jbrowse.xml)
 tool generates a complex JSON data structure using a `configfile` inside the
 XML. This is a much more portable way to deal with that.
 

docs/index.rst

@@ -1,8 +1,3 @@
-.. complexity documentation master file, created by
-   sphinx-quickstart on Tue Jul  9 22:26:36 2013.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
 Welcome to Planemo's documentation!
 ======================================
 

docs/test_format.rst

@@ -306,7 +306,7 @@ option to mount test data into the testing container.
     $ planemo test --engine external_galaxy --galaxy_admin_key <admin_key> --galaxy_user_key <user_key> [--no_shed_install] [--polling_backoff <integer>] --galaxy_url <url>
 
 This is primarily useful for testing workflows against already running Galaxy instances. An admin or
-master API key should be supplied to install missing tool repositories for the workflow and a user API
+bootstrap API key should be supplied to install missing tool repositories for the workflow and a user API
 key should be supplied to run the workflow using. If you wish to skip tool shed repository installation
 (this requires all the tools be present already), use the ``--no_shed_install`` option. If you want to
 reduce the load on the target Galaxy while checking for the status changes use the ``--polling_backoff <integer>``

docs/writing_how_do_i.rst

@@ -32,7 +32,7 @@ Futher reading:
 
 - `bibtex.xml <https://github.com/jmchilton/galaxy/blob/dev/test/functional/tools/bibtex.xml>`__ (test tool with a bunch of random examples)
 - `bwa-mem.xml <https://github.com/jmchilton/bwa-mem/commit/0425264039950bfd9ded06997a08cc8b4ee1ad8f>`__ (BWA-MEM tool by Anton Nekrutenko demonstrating citation of an arXiv article)
-- `macros.xml <https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/vcflib/macros.xml#L15>`__ (Macros for vcflib tool demonstrating citing a github repository)
+- `macros.xml <https://github.com/galaxyproject/tools-iuc/blob/main/tool_collections/vcflib/macros.xml#L16>`__ (Macros for vcflib tool demonstrating citing a github repository)
 
 --------------------------------------------------
 \.\.\. declare a Docker container for my tool?
@@ -69,16 +69,14 @@ Further reading:
 
 - `validator <https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-inputs-param-validator>`__
   XML tag syntax on the Galaxy wiki.
-- `fastq_filter.xml <https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/galaxy_sequence_utils/fastq_filter/fastq_filter.xml>`__
+- `fastq_filter.xml <https://github.com/galaxyproject/tools-iuc/blob/main/tool_collections/galaxy_sequence_utils/fastq_filter/fastq_filter.xml>`__
   (a FASTQ filtering tool demonstrating validator constructs)
-- `gffread.xml <https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/cufflinks/gffread/gffread.xml>`__
+- `gffread.xml <https://github.com/galaxyproject/tools-iuc/blob/main/tools/gffread/gffread.xml>`__
   (a tool by Jim Johnson demonstrating using regular expressions with ``validator`` tags)
 - `code_file.xml <https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/code_file.xml>`__,
   `code_file.py <https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/code_file.py>`__
   (test files demonstrating defining a simple constraint in Python across
   two parameters)
-- `deseq2 tool <https://github.com/bgruening/galaxytools/tree/master/tools/deseq2>`__
-  by Björn Grüning demonstrating advanced ``code`` file validation.
 
 -------------------------------------------------
 \.\.\. check input type in command blocks?
@@ -220,7 +218,7 @@ specify tests for the individual output files using the ``extra_files`` element
 demonstrated by the following tool.
 
 - `composite_output.xml <https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/composite_output.xml>`__
-- `macs_wrapper.xml <https://github.com/galaxyproject/tools-devteam/blob/master/tools/macs/macs_wrapper.xml>`__
+- `macs2_callpeak.xml <https://github.com/galaxyproject/tools-iuc/blob/main/tools/macs2/macs2_callpeak.xml>`__
 
 ------------------------------------------
 \.\.\. test index (\.loc) data?

planemo/context.py

@@ -195,7 +195,7 @@ def configure_standard_planemo_logging(verbose: bool) -> None:
             # examples wrong and should declare their namespaces differently in some way?
             # @mr-c
             # That particular warning is worth suppressing. A PR to silence it permanently would be very welcome!
-            # https://github.com/RDFLib/rdflib/blob/master/rdflib/term.py#L225
+            # https://github.com/RDFLib/rdflib/blob/main/rdflib/term.py
             "rdflib.term": {
                 "handlers": ["console"],
                 "propagate": False,

project_templates/union_bedgraph/bedgraph_examples.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
-wget https://raw.githubusercontent.com/galaxyproject/tools-iuc/master/tools/bedtools/test-data/unionBedGraphs1.bg -o unionBedGraphs1.bedgraph
-wget https://raw.githubusercontent.com/galaxyproject/tools-iuc/master/tools/bedtools/test-data/unionBedGraphs2.bg -o unionBedGraphs2.bedgraph
-wget https://raw.githubusercontent.com/galaxyproject/tools-iuc/master/tools/bedtools/test-data/unionBedGraphs3.bg -o unionBedGraphs3.bedgraph
+wget https://raw.githubusercontent.com/galaxyproject/tools-iuc/main/tools/bedtools/test-data/unionBedGraphs1.bg -o unionBedGraphs1.bedgraph
+wget https://raw.githubusercontent.com/galaxyproject/tools-iuc/main/tools/bedtools/test-data/unionBedGraphs2.bg -o unionBedGraphs2.bedgraph
+wget https://raw.githubusercontent.com/galaxyproject/tools-iuc/main/tools/bedtools/test-data/unionBedGraphs3.bg -o unionBedGraphs3.bedgraph
 unionBedGraphs -i unionBedGraphs1.bedgraph -i unionBedGraphs2.bedgraph -i unionBedGraphs3.bedgraph > output.bedgraph
 
 # planemo tool_init --force --id union_bedgraphs --requirement bedtools --name 'Union Bedgraphs' --example_command 'unionBedGraphs -i unionBedGraphs1.bg -i unionBedGraphs2.bg -i unionBedGraphs3.bg > output.bedgraph' --example_input 'unionBedGraphs1.bg' --example_input 'unionBedGraphs2.bg' --example_input 'unionBedGraphs3.bg' --example_output 'output.bedgraph' --test_case --doi '10.1093/bioinformatics/btq033' --help_text 'Union BedGraphs'

tests/data/data_manager/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py

@@ -319,11 +319,11 @@ def download_from_url(params, tmp_dir, **kwds):
     Download a file from a URL and return a list of filehandles from which to read the data.
 
     >>> tmp_dir = tempfile.mkdtemp()
-    >>> url = 'https://github.com/galaxyproject/tools-iuc/raw/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta/test-data/test.tar.bz2'
+    >>> url = "https://github.com/galaxyproject/tools-iuc/raw/main/data_managers/data_manager_fetch_genome_dbkeys_all_fasta/test-data/test.tar.bz2"
     >>> params = {'param_dict': {'reference_source': {'user_url': url}}}
     >>> fh = download_from_url(params=params, tmp_dir=tmp_dir)[0][0]
     >>> assert fh.readline().startswith('b>FBtr0304171')
-    >>> url = 'https://github.com/galaxyproject/tools-iuc/raw/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta/test-data/phiX174.fasta'
+    >>> url = "https://github.com/galaxyproject/tools-iuc/raw/main/data_managers/data_manager_fetch_genome_dbkeys_all_fasta/test-data/phiX174.fasta"
     >>> params = {'param_dict': {'reference_source': {'user_url': url}}}
     >>> fh = download_from_url(params=params, tmp_dir=tmp_dir)[0][0]
     >>> assert fh.readline().startswith('b>phiX174')

tests/data/repos/bad_repo_name/.shed.yml

@@ -8,5 +8,5 @@ long_description: 'CD-HIT AuxTools is a set of auxiliary programs that can be
   includes programs for removing read duplicates, finding pairs of overlapping
   reads or joining pair-end reads etc.'
 homepage_url: https://github.com/galaxyproject/tools-iuc/
-remote_repository_url: https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_cd_hit_auxtools_0.5_2012_03_07_fix_dan/tool_dependencies.xml
-type: tool_dependency_definition
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/blob/main/packages/package_cd_hit_auxtools_0.5_2012_03_07_fix_dan/tool_dependencies.xml
+type: tool_dependency_definition

tests/data/repos/datamash/.shed.yml

@@ -20,5 +20,5 @@ suite:
   description: datamash performs basic numeric, textual and statistical operations on input textual data files
 name: datamash
 owner: iuc
-remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash
 type: unrestricted