Mercurial > repos > galaxyp > metaquantome_expand
diff metaquantome_expand.xml @ 6:767c1d761aaf draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
| author | galaxyp |
|---|---|
| date | Mon, 18 Mar 2024 12:33:57 +0000 |
| parents | 990b4560ead7 |
| children |
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--- a/metaquantome_expand.xml Wed Jun 16 20:01:14 2021 +0000 +++ b/metaquantome_expand.xml Mon Mar 18 12:33:57 2024 +0000 @@ -1,58 +1,54 @@ <tool id="metaquantome_expand" name="metaQuantome: expand" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> - <description>a set of functional or taxonomy annotations</description> - <macros> - <import>macros.xml</import> - <xml name="FUNC_FILE"> - <param argument="--func_file" type="data" format="tabular" label="Functional file" - help="Tabular file with a peptide sequence column and a functional assignment column with GO terms, EC number, or COG."/> - <param argument="--pep_colname_func" type="text" label="Functional file: peptide column name" value="peptide" - help="The column name within the function file that corresponds to the peptide sequences"> - <validator type="empty_field"/> - </param> - </xml> - <xml name="FUNC_COLNAME"> - <param argument="--func_colname" type="text" label="Functional column name" - help="The column name within the function file with the functional terms"> - <validator type="empty_field"/> - </param> - </xml> - <xml name="TAX_FILE"> - <param argument="--tax_file" type="data" format="tabular" label="Taxonomy assignments file"/> - <param argument="--pep_colname_tax" type="text" label="Taxonomy file: peptide column name" value="peptide" - help="The column name within the taxonomy file that corresponds to the peptide sequences"> - <validator type="empty_field"/> - </param> - </xml> - <xml name="TAX_COLNAME"> - <param argument="--tax_colname" type="text" label="Taxonomy column name"> - <help> + <description>a set of functional or taxonomy annotations</description> + <macros> + <import>macros.xml</import> + <xml name="FUNC_FILE"> + <param argument="--func_file" type="data" format="tabular" label="Functional file" help="Tabular file with a peptide sequence column and a functional assignment column with GO terms, EC number, or COG."/> + <param argument="--pep_colname_func" type="text" label="Functional file: peptide column name" value="peptide" help="The column name within the function file that corresponds to the peptide sequences"> + <validator type="empty_field"/> + </param> + </xml> + <xml name="FUNC_COLNAME"> + <param argument="--func_colname" type="text" label="Functional column name" help="The column name within the function file with the functional terms"> + <validator type="empty_field"/> + </param> + </xml> + <xml name="TAX_FILE"> + <param argument="--tax_file" type="data" format="tabular" label="Taxonomy assignments file"/> + <param argument="--pep_colname_tax" type="text" label="Taxonomy file: peptide column name" value="peptide" help="The column name within the taxonomy file that corresponds to the peptide sequences"> + <validator type="empty_field"/> + </param> + </xml> + <xml name="TAX_COLNAME"> + <param argument="--tax_colname" type="text" label="Taxonomy column name"> + <help> Name of column in taxonomy annotation file that contains the lowest common ancestor (LCA) annotation. The annotations must be either NCBI taxids (strongly preferred) or taxonomy names. </help> - <validator type="empty_field"/> - </param> - </xml> - <xml name="FT_TAR_RANK"> - <param argument="--ft_tar_rank" type="select" label="rank at which to group taxonomy"> - <option value="species">species</option> - <option value="genus" selected="true">genus</option> - <option value="family">family</option> - <option value="order">order</option> - <option value="class">class</option> - <option value="phylum">phylum</option> - <option value="kingdom">kingdom</option> - </param> - </xml> - <token name="@FUNC_FILE@"> + <validator type="empty_field"/> + </param> + </xml> + <xml name="FT_TAR_RANK"> + <param argument="--ft_tar_rank" type="select" label="rank at which to group taxonomy"> + <option value="species">species</option> + <option value="genus" selected="true">genus</option> + <option value="family">family</option> + <option value="order">order</option> + <option value="class">class</option> + <option value="phylum">phylum</option> + <option value="kingdom">kingdom</option> + </param> + </xml> + <token name="@FUNC_FILE@"> --func_file='$mode_args.func_file' --pep_colname_func='$mode_args.pep_colname_func' </token> - <token name="@FUNC_COLNAME@"> + <token name="@FUNC_COLNAME@"> --func_colname='$mode_args.func_colname' </token> - <token name="@ONTOLOGY@"> + <token name="@ONTOLOGY@"> --ontology='$mode_args.ontology_args.ontology' #if $mode_args.ontology_args.ontology == 'go' #if $mode_args.ontology_args.slim_down @@ -60,19 +56,20 @@ #end if #end if </token> - <token name="@TAX_FILE@"> + <token name="@TAX_FILE@"> --tax_file='$mode_args.tax_file' --pep_colname_tax='$mode_args.pep_colname_tax' </token> - <token name="@TAX_COLNAME@"> + <token name="@TAX_COLNAME@"> --tax_colname='$mode_args.tax_colname' </token> - <token name="@FT_TAR_RANK@"> + <token name="@FT_TAR_RANK@"> --ft_tar_rank='$mode_args.ft_tar_rank' </token> - </macros> - <expand macro="requirements" /> - <command detect_errors="exit_code"><![CDATA[ + </macros> + <expand macro="xrefs"/> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ tar -xf '$db_tar' && metaquantome expand --data_dir ./data @@ -97,63 +94,60 @@ #end if --outfile='$outfile' ]]></command> - <inputs> - <param name="db_tar" type="data" format="tar" label="Database Archive File" - help="must be created by 'metaQuantome: download'"/> - <expand macro="SAMPS"/> - <conditional name="mode_args"> - <param argument="--mode" type="select" label="Mode"> - <option value="f">Functional analysis</option> - <option value="t">Taxonomic analysis</option> - <option value="ft">Functional-taxonomic interaction analysis</option> + <inputs> + <param name="db_tar" type="data" format="tar" label="Database Archive File" help="must be created by 'metaQuantome: download'"/> + <expand macro="SAMPS"/> + <conditional name="mode_args"> + <param argument="--mode" type="select" label="Mode"> + <option value="f">Functional analysis</option> + <option value="t">Taxonomic analysis</option> + <option value="ft">Functional-taxonomic interaction analysis</option> + </param> + <when value="f"> + <expand macro="FUNC_FILE"/> + <expand macro="ONTOLOGY_ARGS"/> + <expand macro="FUNC_COLNAME"/> + </when> + <when value="t"> + <expand macro="TAX_FILE"/> + <expand macro="TAX_COLNAME"/> + </when> + <when value="ft"> + <expand macro="FUNC_FILE"/> + <expand macro="FUNC_COLNAME"/> + <expand macro="ONTOLOGY_ARGS"/> + <expand macro="TAX_FILE"/> + <expand macro="TAX_COLNAME"/> + <expand macro="FT_TAR_RANK"/> + </when> + </conditional> + <param argument="--int_file" type="data" format="tabular" label="Intensity file" help=""/> + <param argument="--pep_colname_int" type="text" value="peptide" label="Intensity file: peptide column name" help="The column name within the intensity file that corresponds to the peptide sequences"> + <validator type="empty_field"/> </param> - <when value="f"> - <expand macro="FUNC_FILE"/> - <expand macro="ONTOLOGY_ARGS"/> - <expand macro="FUNC_COLNAME"/> - </when> - <when value="t"> - <expand macro="TAX_FILE"/> - <expand macro="TAX_COLNAME"/> - </when> - <when value="ft"> - <expand macro="FUNC_FILE"/> - <expand macro="FUNC_COLNAME"/> - <expand macro="ONTOLOGY_ARGS"/> - <expand macro="TAX_FILE"/> - <expand macro="TAX_COLNAME"/> - <expand macro="FT_TAR_RANK"/> - </when> - </conditional> - <param argument="--int_file" type="data" format="tabular" label="Intensity file" - help=""/> - <param argument="--pep_colname_int" type="text" value="peptide" label="Intensity file: peptide column name" - help="The column name within the intensity file that corresponds to the peptide sequences"> - <validator type="empty_field"/> - </param> - </inputs> - <outputs> - <data format="tabular" name="outfile" label="${tool.name} on ${on_string} expanded"/> - </outputs> - <tests> - <test> - <param name="db_tar" value="ec.tar" ftype="tar"/> - <param name="samps" value="samples_basic.tab" ftype="tabular"/> - <param name="int_file" value="int_ttest.tab" ftype="tabular"/> - <param name="pep_colname_int" value="peptide" /> - <param name="func_file" value="multiple_func.tab" /> - <param name="pep_colname_func" value="peptide" /> - <param name="func_colname" value="ec"/> - <param name="mode" value="f" /> - <param name="ontology" value="ec" /> - <output name="outfile"> - <assert_contents> - <has_text text="1.2.7.10"/> - </assert_contents> - </output> - </test> - </tests> - <help> + </inputs> + <outputs> + <data format="tabular" name="outfile" label="${tool.name} on ${on_string} expanded"/> + </outputs> + <tests> + <test> + <param name="db_tar" value="ec.tar" ftype="tar"/> + <param name="samps" value="samples_basic.tab" ftype="tabular"/> + <param name="int_file" value="int_ttest.tab" ftype="tabular"/> + <param name="pep_colname_int" value="peptide"/> + <param name="func_file" value="multiple_func.tab"/> + <param name="pep_colname_func" value="peptide"/> + <param name="func_colname" value="ec"/> + <param name="mode" value="f"/> + <param name="ontology" value="ec"/> + <output name="outfile"> + <assert_contents> + <has_text text="1.2.7.10"/> + </assert_contents> + </output> + </test> + </tests> + <help> <![CDATA[ metaQuantome expand =================== @@ -230,5 +224,5 @@ Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues. ]]></help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>