| Previous changeset 5:4187b6df1a40 (2021-06-16) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761 |
|
modified:
macros.xml metaquantome_expand.xml |
| b |
| diff -r 4187b6df1a40 -r 767c1d761aaf macros.xml --- a/macros.xml Wed Jun 16 20:01:14 2021 +0000 +++ b/macros.xml Mon Mar 18 12:33:57 2024 +0000 |
| [ |
| @@ -1,32 +1,37 @@ <macros> <token name="@TOOL_VERSION@">2.0.2</token> <token name="@VERSION_SUFFIX@">0</token> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">metaQuantome</xref> + </xrefs> + </xml> <xml name="requirements"> <requirements> - <requirement type="package" version="@TOOL_VERSION@">metaquantome</requirement> + <requirement type="package" version="@TOOL_VERSION@">metaquantome</requirement> <yield/> </requirements> </xml> <xml name="db"> - <param argument="db_tar" type="data" label="Database Archive File"/> + <param argument="db_tar" type="data" label="Database Archive File"/> </xml> <xml name="ONTOLOGY_ARGS"> - <conditional name="ontology_args"> - <param name="ontology" type="select" label="Ontology"> - <option value="go">Gene Ontology (GO terms)</option> - <option value="ec">Enzyme Commission (EC) numbers</option> - <option value="cog">Clusters of Orthologous Groups (COG categories)</option> - </param> - <when value="go"> - <param argument="--slim_down" type="boolean" label="Use slim GO"/> - </when> - <when value="ec"> - <!-- do nothing --> - </when> - <when value="cog"> - <!-- do nothing --> - </when> - </conditional> + <conditional name="ontology_args"> + <param name="ontology" type="select" label="Ontology"> + <option value="go">Gene Ontology (GO terms)</option> + <option value="ec">Enzyme Commission (EC) numbers</option> + <option value="cog">Clusters of Orthologous Groups (COG categories)</option> + </param> + <when value="go"> + <param argument="--slim_down" type="boolean" label="Use slim GO"/> + </when> + <when value="ec"> + <!-- do nothing --> + </when> + <when value="cog"> + <!-- do nothing --> + </when> + </conditional> </xml> <token name="@COMMON_PARAMS@"><![CDATA[ --samps '$samps' @@ -40,12 +45,12 @@ ]]> </token> <xml name="SAMPS"> - <param name="samps" type="data" format="tabular" label="Samples file" - help="must be created by 'metaQuantome: create samples file'"/> + <param name="samps" type="data" format="tabular" label="Samples file" help="must be created by 'metaQuantome: create samples file'"/> </xml> <xml name="citations"> <citations> - <yield /> + <citation type="doi">10.1021/ACS.JPROTEOME.0C00960</citation> + <yield/> </citations> </xml> </macros> |
| b |
| diff -r 4187b6df1a40 -r 767c1d761aaf metaquantome_expand.xml --- a/metaquantome_expand.xml Wed Jun 16 20:01:14 2021 +0000 +++ b/metaquantome_expand.xml Mon Mar 18 12:33:57 2024 +0000 |
| [ |
| b'@@ -1,58 +1,54 @@\n <tool id="metaquantome_expand" name="metaQuantome: expand" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n- <description>a set of functional or taxonomy annotations</description>\n- <macros>\n- <import>macros.xml</import>\n- <xml name="FUNC_FILE">\n- <param argument="--func_file" type="data" format="tabular" label="Functional file"\n- help="Tabular file with a peptide sequence column and a functional assignment column with GO terms, EC number, or COG."/>\n- <param argument="--pep_colname_func" type="text" label="Functional file: peptide column name" value="peptide"\n- help="The column name within the function file that corresponds to the peptide sequences">\n- <validator type="empty_field"/>\n- </param>\n- </xml>\n- <xml name="FUNC_COLNAME">\n- <param argument="--func_colname" type="text" label="Functional column name"\n- help="The column name within the function file with the functional terms">\n- <validator type="empty_field"/>\n- </param>\n- </xml>\n- <xml name="TAX_FILE">\n- <param argument="--tax_file" type="data" format="tabular" label="Taxonomy assignments file"/>\n- <param argument="--pep_colname_tax" type="text" label="Taxonomy file: peptide column name" value="peptide"\n- help="The column name within the taxonomy file that corresponds to the peptide sequences">\n- <validator type="empty_field"/>\n- </param>\n- </xml>\n- <xml name="TAX_COLNAME">\n- <param argument="--tax_colname" type="text" label="Taxonomy column name">\n- <help>\n+ <description>a set of functional or taxonomy annotations</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ <xml name="FUNC_FILE">\n+ <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."/>\n+ <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">\n+ <validator type="empty_field"/>\n+ </param>\n+ </xml>\n+ <xml name="FUNC_COLNAME">\n+ <param argument="--func_colname" type="text" label="Functional column name" help="The column name within the function file with the functional terms">\n+ <validator type="empty_field"/>\n+ </param>\n+ </xml>\n+ <xml name="TAX_FILE">\n+ <param argument="--tax_file" type="data" format="tabular" label="Taxonomy assignments file"/>\n+ <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">\n+ <validator type="empty_field"/>\n+ </param>\n+ </xml>\n+ <xml name="TAX_COLNAME">\n+ <param argument="--tax_colname" type="text" label="Taxonomy column name">\n+ <help>\n Name of column in taxonomy annotation file that contains\n the lowest common ancestor (LCA) annotation. The annotations must\n be either NCBI taxids (strongly preferred) or taxonomy\n names.\n </help>\n- <validator type="empty_field"/>\n- </param>\n- </xml>\n- <xml name="FT_TAR_RANK">\n- <param argument="--ft_tar_rank" type="select" label="rank at which to group taxonomy">\n- <option value="species">species</option>\n- <option value="genus" selected="true">genus</option>\n- <option value="family">family</option>\n- <option value="order">order</option>\n- <option value="class">class</option>\n- <option value="phylum">phylum</option>\n- <option value="kingdom">kingdom</option>\n- </param>\n- </xml>\n- <token nam'..b' <expand macro="ONTOLOGY_ARGS"/>\n+ <expand macro="FUNC_COLNAME"/>\n+ </when>\n+ <when value="t">\n+ <expand macro="TAX_FILE"/>\n+ <expand macro="TAX_COLNAME"/>\n+ </when>\n+ <when value="ft">\n+ <expand macro="FUNC_FILE"/>\n+ <expand macro="FUNC_COLNAME"/>\n+ <expand macro="ONTOLOGY_ARGS"/>\n+ <expand macro="TAX_FILE"/>\n+ <expand macro="TAX_COLNAME"/>\n+ <expand macro="FT_TAR_RANK"/>\n+ </when>\n+ </conditional>\n+ <param argument="--int_file" type="data" format="tabular" label="Intensity file" help=""/>\n+ <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">\n+ <validator type="empty_field"/>\n </param>\n- <when value="f">\n- <expand macro="FUNC_FILE"/>\n- <expand macro="ONTOLOGY_ARGS"/>\n- <expand macro="FUNC_COLNAME"/>\n- </when>\n- <when value="t">\n- <expand macro="TAX_FILE"/>\n- <expand macro="TAX_COLNAME"/>\n- </when>\n- <when value="ft">\n- <expand macro="FUNC_FILE"/>\n- <expand macro="FUNC_COLNAME"/>\n- <expand macro="ONTOLOGY_ARGS"/>\n- <expand macro="TAX_FILE"/>\n- <expand macro="TAX_COLNAME"/>\n- <expand macro="FT_TAR_RANK"/>\n- </when>\n- </conditional>\n- <param argument="--int_file" type="data" format="tabular" label="Intensity file"\n- help=""/>\n- <param argument="--pep_colname_int" type="text" value="peptide" label="Intensity file: peptide column name"\n- help="The column name within the intensity file that corresponds to the peptide sequences">\n- <validator type="empty_field"/>\n- </param>\n- </inputs>\n- <outputs>\n- <data format="tabular" name="outfile" label="${tool.name} on ${on_string} expanded"/>\n- </outputs>\n- <tests>\n- <test>\n- <param name="db_tar" value="ec.tar" ftype="tar"/>\n- <param name="samps" value="samples_basic.tab" ftype="tabular"/>\n- <param name="int_file" value="int_ttest.tab" ftype="tabular"/>\n- <param name="pep_colname_int" value="peptide" />\n- <param name="func_file" value="multiple_func.tab" />\n- <param name="pep_colname_func" value="peptide" />\n- <param name="func_colname" value="ec"/>\n- <param name="mode" value="f" />\n- <param name="ontology" value="ec" />\n- <output name="outfile">\n- <assert_contents>\n- <has_text text="1.2.7.10"/>\n- </assert_contents>\n- </output>\n- </test>\n- </tests>\n- <help>\n+ </inputs>\n+ <outputs>\n+ <data format="tabular" name="outfile" label="${tool.name} on ${on_string} expanded"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="db_tar" value="ec.tar" ftype="tar"/>\n+ <param name="samps" value="samples_basic.tab" ftype="tabular"/>\n+ <param name="int_file" value="int_ttest.tab" ftype="tabular"/>\n+ <param name="pep_colname_int" value="peptide"/>\n+ <param name="func_file" value="multiple_func.tab"/>\n+ <param name="pep_colname_func" value="peptide"/>\n+ <param name="func_colname" value="ec"/>\n+ <param name="mode" value="f"/>\n+ <param name="ontology" value="ec"/>\n+ <output name="outfile">\n+ <assert_contents>\n+ <has_text text="1.2.7.10"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help>\n <![CDATA[\n metaQuantome expand\n ===================\n@@ -230,5 +224,5 @@\n \n Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.\n ]]></help>\n- <expand macro="citations" />\n+ <expand macro="citations"/>\n </tool>\n' |