Tmtanalyst

tools/interactivetool_tmtanalyst/interactivetool_tmtanalyst.xml

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+<tool id="interactive_tool_tmtanalyst" tool_type="interactive" name="TMT Analyst" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
+    <description>Analyze and Visualize Label-Free Proteomics output from MaxQuant</description>
+
+    <xrefs>
+        <!-- TMT-analyst oesn't appear to be in bio.tools -->
+        <!-- <xref type="bio.tools">LFQ-Analyst</xref> -->
+    </xrefs>
+
+    <macros>
+        <token name="@TOOL_VERSION@">0.9.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PORT@">8000</token>
+    </macros>
+
+    <edam_topics>
+        <edam_topic>topic_0121</edam_topic>
+    </edam_topics>
+
+    <edam_operations>
+        <edam_operation>operation_3214</edam_operation>
+    </edam_operations>
+
+    <requirements>
+        <!-- this container has port 8888 exposed -->
+        <container type="docker">haileyzhang/tmt-analyst:v@TOOL_VERSION@</container>
+    </requirements>
+
+    <entry_points>
+        <entry_point name="TMT-analyst" requires_domain="True">
+            <port>@PORT@</port>
+        </entry_point>
+    </entry_points>
+
+    <command detect_errors="exit_code"><![CDATA[
+
+cp '$run_tmtanalyst' '$outfile' &&
+cd /srv/shiny-server/tmt-analyst &&
+Rscript '$run_tmtanalyst'
+
+    ]]></command>
+
+    <configfiles>
+        <configfile name="run_tmtanalyst"><![CDATA[
+## wrapper to run LFQAnalyst from the shiny-server directory
+source('runApp.R')
+options(shiny.port=@PORT@)
+
+TMTAnalyst(protein_path="$protein_groups", exp_path="$design")
+
+        ]]></configfile>
+    </configfiles>
+
+    <inputs>
+        <param name="protein_groups" type="data" format="txt" label="ProteinGroups.txt" help="" />
+        <param name="design" type="data" format="txt" label="Experimental Design Matrix" help="" />
+    </inputs>
+
+    <outputs>
+        <data name="outfile" format="txt"
+          label="${tool.name} on ${on_string}: Rscript" />
+    </outputs>
+
+    <tests>
+        <!-- Hint: You can use [ctrl+alt+t] after defining the inputs/outputs to auto-scaffold some basic test cases. -->
+    </tests>
+
+    <help><![CDATA[
+
+.. class:: infomark
+
+LFQ-Analyst
+===========
+
+A tool for analysing label-free quantitative proteomics dataset
+https://bioinformatics.erc.monash.edu/apps/LFQ-Analyst/
+
+
+Motivation
+----------
+
+-  Automate downstream statistical analysis of Label free quantitative
+   proteomics data (generated by MaxQuant)
+
+Input
+-----
+
+-  MaxQuant **proteinGroups.txt** file
+-  An experiment design table (tab separated file) containing three
+   columns (“label”, “condition”, “replicate”)
+
+Data pre-filtering criteria
+---------------------------
+
+-  Remove potential contaminants
+-  Remove reverse sequences
+-  Remove proteins identified only by sites
+-  Remove proteins identified/quantified by a single Razor or unique
+   peptide
+-  Remove observation with high proportion of missing values (intensity
+   values must be present at least 2 out of three replicates)
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1021/acs.jproteome.9b00496</citation>
+    </citations>
+</tool>

tools/interactivetool_tmtanalyst/test-data/experimental_design_example.txt

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+label	condition	replicate
+Total_309B	Benign	1
+Total_309M	Malignant	1
+Total_445B	Benign	2
+Total_445M	Malignant	2
+Total_555B	Benign	3
+Total_555M	Malignant	3
+Total_588B	Benign	4
+Total_588M	Malignant	4
+Total_636B	Benign	5
+Total_636M	Malignant	5
+Total_667B	Benign	6
+Total_667M	Malignant	6
+Total_741B	Benign	7
+Total_741M	Malignant	7
+Total_764B	Benign	8
+Total_764M	Malignant	8
+Total_876B	Benign	9
+Total_876M	Malignant	9
+Total_883B	Benign	10
+Total_883M	Malignant	10