Cpc2 package

tools/cpc2/.shed.yml

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+name: cpc2
+owner: galaxy-australia
+description: Coding Potential Calculator.
+homepage_url: http://cpc2.gao-lab.org/index.php
+long_description: |
+    A fast and accurate coding potential calculator based on sequence intrinsic features..
+remote_repository_url: https://github.com/mthang/galaxy-local-tools/tree/cpc2/tools/cpc2
+type: unrestricted
+categories:
+- Assembly

tools/cpc2/cpc2.xml

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+<tool id="cpc2" name="Coding Potential Calculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Fast and accurate coding potential calculator based on sequence intrinsic features</description>
+    <macros>
+	  <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="xrefs"/>
+    <expand macro="stdio" />
+    <command><![CDATA[
+	    touch 'output' &&
+	    CPC2.py 
+	    -i $sequence
+	    -o output &&
+	    cp 'output.txt' '$result'
+	    2>&1
+
+    ]]></command>
+    <inputs>
+	    <param name="sequence" type="data" format="fasta" label="Input Sequence" help="Sequences for Coding Potential Calculator"/>
+    </inputs>
+    <outputs>
+	    <data name="result" format="txt" label="${tool.name} on ${on_string}: Coding Potential Statistic"/>
+    </outputs>
+
+    <tests>
+	 <test>
+              <!-- #1 test on forward strand only -->
+              <param name="sequence" value="example.fa" ftype="fasta"/>
+              <output name="result" file="forward_only.tsv" ftype="tsv"/>
+        </test> 
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+Coding Potential Calculator. Fast and accurate coding potential calculator based on sequence intrinsic features.
+
+**Input**
+
+- input file: a sequence file (fasta format)
+
+**Parameters**
+
+- ORF : 
+
+**Output**
+
+- coverage_stats.csv
+
+.. class:: infomark
+
+**References**
+
+]]></help>
+     <citations>
+        <citation type="doi">DOI: 10.1093/nar/gkx428</citation>
+    </citations>
+</tool>

tools/cpc2/macros.xml

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+<macros>
+    <token name="@TOOL_VERSION@">1.0.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">20.09</token>
+    <xml name="requirements">
+        <requirements>
+		<requirement type="package" version="@TOOL_VERSION@">cpc2</requirement>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+      <stdio>
+         <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
+         <exit_code range="1:"  level="fatal" description="Error" />
+      </stdio>
+    </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">cpc2</xref>
+        </xrefs>
+    </xml>
+</macros>

tools/cpc2/test-data/example.fa

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+>AF282387 Filobasidiella neoformans calcineurin B regulatory subunit (CNB1) mRNA, complete cds
+ATGGGTGCCGCTGAATCCTCCATGTTCAACTCTCTGGAGAAGAACTCCAACTTCTCAGGACCGGAGCTTA
+TGAGGTTGAAGAAGAGGTTCATGAAGCTTGACAAGGACGGTTCCGGATCGATTGACAAAGACGAGTTTCT
+TCAGATCCCTCAAATCGCGAATAACCCTTTGGCGCATCGAATGATAGCAATCTTTGATGAAGATGGAAGT
+GGAACGGTTGACTTCCAAGAATTTGTCGGAGGTTTGAGCGCTTTCAGTAGTAAAGGAGGTCGTGATGAGA
+AGCTGAGATTCGCTTTCAAGGTGTACGACATGGATCGAGACGGCTACATCTCTAACGGTGAACTGTATCT
+TGTGTTGAAGCAAATGGTCGGAAATAACCTTAAAGACCAACAATTGCAACAAATTGTAGACAAAACCATC
+ATGGAGGCTGACAAGGACGGGGATGGAAAGCTCTCTTTTGAGGAGTTCACACAAATGGTCGCCAGCACAG
+ATATTGTGAAGCAAATGACCCTTGAAGATCTTTTCTAA
+
+>Tsix_mus NR_002844.1 Mus musculus X (inactive)-specific transcript, antisense (Tsix) on chromosome X
+GTGTGTTCATGCGTGCGCACGTGTACCCGTGCGTCCACACTCCGCCAGCACGTGTGCTAGCTTGCAAGTT
+TTCAGTTTGAGTACAGACACCAGGCCATAGCCCAATGGCAGCAGTGACAGGGAGGACCGTGGCAGCATGT
+TACAATCAGAAGACAACTTCCGGATTTTCACTCTGTCCTAAAAAGGTGGTCAAGTGTGCTAACCACACCC
+TCTCAGCAGGATCCCGCGCCTCAAGAGCCTTAGGTCCCGCCCCACACTCCCTCAAACCCTCAGTGCAGCG
+CTTGTGTCAGGCGCAATCTCGCAAGATCCGGTGAGGCGCTACGTCGTGCTCCACTCGGTCCCAAAAGTAC
+CTGCAAGCGCTACACACTTGCGCTCGGCGCCCTTGCTCTGTTCTCACTTTCCGAGATATCCACGCATCTT
+GAGTCCTGCATCCACTCCCGGGAGGCGGCTGCGGCAAGCGCGTGATGGAAGAAGAGCGTGATAGCCAGCT
+AGACAGGTGGCCAGAGCGGAGCGGACAGTGGAGCGATGGCTACGTGCTTGCGGGACAGCGGAAGAGATGG
+TTAAAGTGATTGCCAAGCAGCAGAAAGATTCCTAAAATGCTTGCCAGCTATGCGGAGATGAAGGTGAGGT
+TTCAATGATTTACATCGACCAAGAACCCGCAGCCTCGGTCTCTCGAATCGGATCCGACATCATCCAACAC
+TTCAGTGTTAGAATTGCAAGCATGCGCTCTCCCGACCTGGGCAGGCACTTCGAAAAAATGATGACTAAAG
+ACACACGTGAAGTACCAAGCGAAACTCACGTCCTTATGGGACAGTGACTCATCACAGTCTAATTCCATCC
+TGGCCACCAAGCAATAATGCACATTTCTAACTGGAAGTCAAGCAAACACCAACACTTTCACACTTGTGCC
+CATTTCTGACGAGTTACGTCAAGTGGCAACCAACACTTCCACTTAGCCTTGCCTCAGCTTCGAGTGGCAC
+AAGGTAGGACCAACCACACCCTACCATAATGCACCAAGTGTACCCTCGGGCAAAGCCCGCCAAGTAGCTA
+AAGCCCGCCAAAAAAAAAATCACTGAAAGAAACCACTAGAGGGCAGGTCACATGACTTCCGCCATCTTAG
+ACACATTCAAGAGCATGTGCCACCTCTCCAGGCTAACTCAGACATGAAGCTGACATGTGACACACAAAGC
+CCTTTGCGTTATACCGCACCAAGAACTTGAGCCGCCATCTTTTCCTGTACGACCTAAATGTCCTATAATC
+CATTGCTACACACCAGAACAAAGATTGGGCTGTCGAGCCTCGGGTGGAGCCCCCGAGCCGCCATTTTATA
+GACTTCTGAGCAGCCCTTAAAGCCACGGGGGACCGCGCCAGGGGTCCATATGCACACACACCCTGCCCAA
+TCCCCACACCCACGCTGAGCCCTATCCCCTAGTCCTCTGCGGCTTCCGCGCAACACCGCACACTAATACG
+AGCACTCCTTGGCTTTCTCTTCCGGCTAGCACAACCCCGCAAATGCTACCACAAATCAAGGCGAATCCCG
+CAACCCCGCACATATAAAGAAAGCCTTTAGCTAGCGCAGCGCAATTGGTTGCTTTTATCCAGTCCGCTGT
+GCTCCTCGGTGTCCTAATTCTTGGCGTAACTGGCTCGAGAATAGCCGTATCACGCAGAAGCCATAATGGC
+GGACGCGGGCTCTCCACGCCCTGAACACCCACTCAGTTTAAGAGCAAAGTCGTTTTTCTAAGCCATAGGT
+TCACTCACACAGCACCAAACGATCAGCAGCAACAGTACACGCAAATAAGAGGCATAGATATTCCAGGTAG
+TGCAATAACTCACAAAACCATATTTCCATCCACCAAGCCCCGTTGGGCCTGTAAAAAAAAAATTTAAAGC
+AGGTATCCACAGCCCCGATGGGCAAAAGAAAAAGAAAAAAAAATAATAACAGCAGGTATCCGAGGCCCCG
+TTGGGCATGGGAAAAAAAGACTAAACGCAGGTATCCGAGGTCCCGATGGACCGAGAAAGGTTTTTTTTTT
+TTTTTTTTTTTTTACAAAAAGCAGGTATCCATGGCCCCGATGGGCTAAGGAGAAGAAAAAAAGAATAAAA
+GCAGGTATCCACAGCCCAGATGGGCAAGTTTAGAAAAAAAAATAATAAGAAAAAAAAAGAATGAAAAGGC
+AGGTAAGTATCCAAAACCCCGTTGGGCATGGAATGGCGGGGAGGACACACAGGTATCCGTGGCCCCGATG
+GGCAAGATTATATAAACAATGAAAGAAAGGTAAGTCCACCATACACACACAAGTATCAACCAAAAGGCAC
+AACAAAGAAATATTCCTTAAAAATGAAAAATTGACTGAAAATATTACAAATATCAAAAAGTATGGAGGAC
+ATGTCAAAAAAAAAATCTTACCAGAACATATCAAAACGTCAAAAATCTCGTGGAATTTTGATATGTTTTC
+TTAAATAAGCCATAAGGCTTGGTGGTAGGGGAACTAAAAATGTTCCCCCAAAGCTCCTTAGATGGAGAGA
+AACCACGGAAGAACCGCACATCCACGGGAAACGAGCAAACATGGCTGGAGCAAGCCGTTGCACGCCTTTA
+ACTGATCCGCGGCGCTGAAGGCGGAGAGACCAGAAGAGGAGTGGCCACAAAGATTGCAATTCTGACATCT
+TATTGGACCTTTAGGTCTAACTATATTATAAAAAAATTAAAATGAATAAAGATGGAGGTACGTAAGCTCA
+GTGACATGACGCGTGAATTTCATTATTTTGCGCGATAATGAAGGATTATCCTATTTTACAGCTAAAAACG
+TTTATGTAGAACTTCACATAAACATTTGGGTGTGTACATTTAGCACACACCTGTCTATGCAAAATTTCAA
+TATATCTTCTACTTGGACAAACCATGTGTCGCTCCGGTCTTGGACACTAGAAGTTCTTCTGCATTAGTTG
+GCGACCTCAGATGAGGAGAGGAAAGGGTAGAAATGCCTCACAAAATGGCTCCTTGGTTCCTAAATTATCA
+GAGTATTAGTTGTGACCGATTTGGAGGGCTTACGCTCATAGTTTTGGGTCATTGGCATCTTAGTCTTTCT
+CTGGGAACCTGGTGACTCCATACCTTGGGACAAAAACGCACTGAAGACGTTACTAGCTAGCAGTAATGAA
+AAATAATTCCTAAATGCCAAAGCAAAGCCTTAGGGAATAATAGCTCATTGGTATCTTACTCGCCCCAGAG
+ACACTGCTAACTTAAAAGAACTGTCAAATTTTGTTAACTGTCAAACTATGAATATCCACATGAAAGAGAT
+CAGACACCCTGGGTATTAGAAAATCAAAGGATATGTTGTCTCGTTGATCACGCTGACAAATAATTCACAG
+TCTGTTCTAAGTTCCCTTTAGGCGTCCCATGAATAATAAAGGACACAAAATTGGTTTGCTTATGGACGAT
+CAAAGTGCCAGCAATTCAGTAATCTTACTATTGAGGTGGTTCAGGTAGGGATGGAAAAATATCTGCTACA
+AAATAAACAGTTTCAACCAAAAGAAAAACAAATTAACAAGGTAAATAAATGATGCACACAGACTGAATAA
+ACCAGCAGGTGGCAGCATGAATCTTTCCAAGGCATCTGAAGCCAAACTTGGAGTGCAAAAGGATTCCTAT
+CTGAATTGAGAAGTAAAGGTTACTTTGTCTAACTTTAGTTGACAGAGCGATCAGGATCAGAGTAACAAGC
+ACACCAAAAGCATCACCAGTGAGAAGTCACATAGGACATATTAGGGAAAAAAGACCCAAGGAAGGGCTCT
+TCACAGCTAAGAGCACCTGGCTCCACGATGGATATGGCTTTGTATAAACGAGAACTTCTAAATGAGCTGT
+ACAAAGAGAATTTAGAACTTGCGAGGTACTGGTCACAGATTATGCAAGCCAGTGTATCATTTTTGTGGGG
+ATGCTAGAGAGAATCATCAAATTAAAGAGTTAAATTTAGTCTCTGTGTTTTACTTAGTCCCAATTCTTGC
+AAAGGTCATCATTCTTTCTCACACCGTGTACATCAAGGTATGTCAGGTTTCGGGGACACTTTTTAGTCTT
+ATCACAAGAAAGCATGAAGGGATATGTGCTAAAACTCAGTTCCTGGGCTGGAGAGATAGCTCAGTGGTTA
+GGAGTGCTGACTGCTCTTCCAGAGGGCCTGAGTTCAATTCTCAACAACTTCGTTGTGGCTCACAGTCATC
+TGTAGTGGGGGATCCGATATCTAACCTTCTTCTGATGTATCTGAACAGTGACCGACAGTGTACTCACATT
+AAATAAATATTTTTCTAAAAAACACCTCCA

tools/cpc2/test-data/forward_only.tsv

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+#ID	transcript_length	peptide_length	Fickett_score	pI	ORF_integrity	coding_probability	label
+AF282387	528	176	0.47841	4.67108154297	1	0.997542	coding
+Tsix_mus	4300	70	0.28464	11.0512084961	1	0.0447346	noncoding

tools/cpc2/test-data/forward_reverse.tsv

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+#ID	transcript_length	peptide_length	Fickett_score	pI	ORF_integrity	coding_probability	label
+AF282387	528	176	0.47841	4.67108154297	1	0.997542	coding
+Tsix_mus	4300	80	0.28464	11.7931518555	1	0.0521955	noncoding