Mercurial > repos > galaxyp > pyteomics_mztab2tsv
diff mztab2tsv.xml @ 0:a46d857e25c2 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
| author | galaxyp |
|---|---|
| date | Fri, 15 Jan 2021 15:57:59 +0000 |
| parents | |
| children | dc31e153fe6c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mztab2tsv.xml Fri Jan 15 15:57:59 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=""""/></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=""""/></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> \ No newline at end of file