Mercurial > repos > galaxyp > metaquantome_expand

changeset 6:767c1d761aaf draft default tip

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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 4187b6df1a40
children
files macros.xml metaquantome_expand.xml
diffstat 2 files changed, 127 insertions(+), 128 deletions(-) [+]
line wrap: on
line diff
--- 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>
--- 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>