| Previous changeset 5:860429737408 (2021-06-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761 |
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modified:
macros.xml metaquantome_db.xml |
| b |
| diff -r 860429737408 -r e63db1aa82ee macros.xml --- a/macros.xml Wed Jun 16 20:00:49 2021 +0000 +++ b/macros.xml Mon Mar 18 12:34:24 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> |
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| diff -r 860429737408 -r e63db1aa82ee metaquantome_db.xml --- a/metaquantome_db.xml Wed Jun 16 20:00:49 2021 +0000 +++ b/metaquantome_db.xml Mon Mar 18 12:34:24 2024 +0000 |
| [ |
| @@ -3,7 +3,8 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="xrefs"/> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ mkdir -p data && #set $database_list = str($databases).split(',') @@ -14,26 +15,25 @@ tar --create --file '$outfile' data ]]></command> <inputs> - <param name="databases" type="select" multiple="True" display="checkboxes" - label="Databases to Download"> - <option value="ncbi" selected="true">NCBI Taxonomy Database</option> - <option value="go" selected="true">Gene Ontology Database</option> - <option value="ec" selected="true">Enzyme Commission (EC) database</option> + <param name="databases" type="select" multiple="True" display="checkboxes" label="Databases to Download"> + <option value="ncbi" selected="true">NCBI Taxonomy Database</option> + <option value="go" selected="true">Gene Ontology Database</option> + <option value="ec" selected="true">Enzyme Commission (EC) database</option> </param> </inputs> <outputs> <data format="tar" name="outfile" label="metaquantome databases"/> </outputs> <tests> - <test> - <param name="databases" value="go"/> - <output name="outfile"> - <assert_contents> - <has_text text="ontology: go"/> - <has_text text="ontology: go/subsets/goslim_metagenomics"/> - </assert_contents> - </output> - </test> + <test> + <param name="databases" value="go"/> + <output name="outfile"> + <assert_contents> + <has_text text="ontology: go"/> + <has_text text="ontology: go/subsets/goslim_metagenomics"/> + </assert_contents> + </output> + </test> </tests> <help> <![CDATA[ @@ -69,5 +69,5 @@ Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues. ]]></help> - <expand macro="citations" /> + <expand macro="citations"/> </tool> |