--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mztab2tsv.xml	Fri Jan 15 15:58:54 2021 +0000
@@ -0,0 +1,98 @@
+<tool id="mztab2tsv" name="pyteomics" version="@TOOL_VERSION@" profile="20.01" license="MIT">
+    <description>convert mztab to tabular</description>
+    <macros>
+        <token name="@TOOL_VERSION@">4.4.1</token>
+        <xml name="output" token_type="" token_label="">
+            <data name="out_@TYPE@" format="tabular" from_work_dir="@TYPE@.tsv" label="${tool.name} on ${on_string}: @LABEL@">
+                <filter>"@TYPE@" in out_select</filter>
+            </data>
+        </xml>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">pyteomics</xref>
+    </xrefs>
+    <edam_topics>
+        <edam_topic>topic_0121</edam_topic><!-- proteomics -->
+        <edam_topic>topic_3520</edam_topic><!-- proteomics experiment-->
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_3434</edam_operation><!--	Convert a data set from one form to another -->
+    </edam_operations>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">pyteomics</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    ## make sure that selected outputs exist even if the tool does not generate them
+    #for o in $out_select
+        touch '$o'.tsv &&
+    #end for
+    '$__tool_directory__/mztab_reader.py' --path_in '$path_in'
+    ]]></command>
+    <inputs>
+        <param argument="--path_in" type="data" format="mztab,mztab2" label="mztab or mztab2 data set" help="" />
+        <param name="out_select" type="select" label="Select desired tables" multiple="true" help="">
+            <option value="mtd" selected="true">Metadata (v1,v2)</option>
+            <option value="prt">Protein table (v1)</option>
+            <option value="pep">Peptide table (v1)</option>
+            <option value="psm">Peptide spectrum match table (v1)</option>
+            <option value="sml">Small molecule table (v1,v2)</option>
+            <option value="smf">Small molecule feature table (v2)</option>
+            <option value="sme">Small molecule evidence table (v2)</option>
+        </param>
+    </inputs>
+    <outputs>
+        <expand macro="output" type="mtd" label="Metadata"/>
+        <expand macro="output" type="prt" label="Proteins"/>
+        <expand macro="output" type="pep" label="Peptides"/>
+        <expand macro="output" type="psm" label="Peptide spectrum matches"/>
+        <expand macro="output" type="sml" label="Small molecules"/>
+        <expand macro="output" type="smf" label="Small molecule feature"/>
+        <expand macro="output" type="sme" label="Small molecule evidence"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="5">
+            <param name="path_in" ftype="mztab" value="1.mztab"/>
+            <param name="out_select" value="mtd,prt,pep,psm,sml"/>
+            <output name="out_mtd" ftype="tabular">
+                <assert_contents><has_text text="mzTab-version"/></assert_contents>
+            </output>
+            <output name="out_prt" ftype="tabular">
+                <assert_contents><has_text text="accession"/></assert_contents>
+            </output>
+            <output name="out_pep" ftype="tabular">
+                <assert_contents><has_text text="&quot;&quot;"/></assert_contents>
+            </output>
+            <output name="out_psm" ftype="tabular">
+                <assert_contents><has_text text="PSM_ID"/></assert_contents>
+            </output>
+            <output name="out_sml" ftype="tabular">
+                <assert_contents><has_text text="&quot;&quot;"/></assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="4">
+            <param name="path_in" ftype="mztab" value="2.mztab"/>
+            <param name="out_select" value="mtd,sml,smf,sme"/>
+            <output name="out_mtd" ftype="tabular">
+                <assert_contents><has_text text="mzTab-version"/></assert_contents>
+            </output>
+            <output name="out_sml" ftype="tabular">
+                <assert_contents><has_text text="SML_ID"/></assert_contents>
+            </output>
+            <output name="out_smf" ftype="tabular">
+                <assert_contents><has_text text="SMF_ID"/></assert_contents>
+            </output>
+            <output name="out_sme" ftype="tabular">
+                <assert_contents><has_text text="SME_ID"/></assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Convert a mztab or mztab2 file to tabular files using the pyteomics library https://pyteomics.readthedocs.io/en/latest/.
+
+        The specifications of the mztab and mztab2 formats can be found here https://github.com/HUPO-PSI/mzTab/.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1007/s13361-012-0516-6</citation>
+        <citation type="doi">10.1021/acs.jproteome.8b00717</citation>
+    </citations>
+</tool>
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