diff scanpy-filter-genes.xml @ 1:7aebd6265a97 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"

--- a/scanpy-filter-genes.xml	Wed Apr 03 11:10:01 2019 -0400
+++ b/scanpy-filter-genes.xml	Mon Sep 16 08:15:32 2019 -0400
@@ -2,42 +2,50 @@
 <tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy1">
   <description>based on counts and numbers of cells expressed</description>
   <macros>
-    <import>scanpy_macros.xml</import>
+    <import>scanpy_macros2.xml</import>
   </macros>
   <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 ln -s '${input_obj_file}' input.h5 &&
-PYTHONIOENCODING=utf-8 scanpy-filter-genes.py
-    -i input.h5
-    -f '${input_format}'
-    -o output.h5
-    -F '${output_format}'
-    #if $parameters
-    #set pars = ','.join([str($p['name']) for $p in $parameters])
-        -p '${pars}'
-    #set mins = ','.join([str($p['min']) for $p in $parameters])
-        -l '${mins}'
-    #set maxs = ','.join([str($p['max']) for $p in $parameters])
-        -j '${maxs}'
-    #end if
-    #if $subset
-        -s '${subset}'
-    #end if
-    @EXPORT_MTX_OPTS@
+PYTHONIOENCODING=utf-8 scanpy-filter-genes
+#if $parameters
+    #set pars = ' '.join(['--param {name} {min} {max}'.format(**$p) for $p in $parameters])
+    ${pars}
+#end if
+#if $categories
+    #set cats = ' '.join(['--category {name} {values}'.format(**$c) for $c in $categories])
+    ${cats}
+#end if
+#if $subsets
+    #set subs = ' '.join(['--subsets {name} {subset}'.format(**$s) for $c in $subsets])
+    ${subs}
+#end if
+    @INPUT_OPTS@
+    @OUTPUT_OPTS@
 ]]></command>
 
   <inputs>
     <expand macro="input_object_params"/>
     <expand macro="output_object_params"/>
-    <repeat name="parameters" title="Parameters used to filter genes" min="1">
-      <param name="name" type="text" value="n_cells" label="Name of parameter to filter on" help="for example n_cells or n_counts">
+
+    <repeat name="parameters" title="Parameters used to filter cells" min="1">
+      <param name="name" type="text" value="n_cells" label="Name of parameter to filter on" help="for example n_genes or n_counts">
         <option value="n_cells">n_cells</option>
-        <option value="n_counts">n_counts</option>
+        <option value="gene:n_counts">n_counts</option>
       </param>
-      <param name="min" type="float" value="0" min="0" label="Min value"/>
-      <param name="max" type="float" value="1e9" label="Max value"/>
+      <param name="min" type="float" min="0" value="0" label="Min value"/>
+      <param name="max" type="float" min="0" value="1e9" label="Max value"/>
     </repeat>
-    <param name="subset" argument="--subset-list" type="data" format="tsv" optional="true" label="List of gene IDs or symbols"/>
+
+    <repeat name="categories" title="Categories used to filter genes" min="0">
+      <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
+      <param name="values" type="text" value="" label="Comma-separated values"/>
+    </repeat>
+
+    <repeat name="subsets" title="Subsets used to filter genes" min="0">
+      <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
+      <param name="subset" type="data" format="tabular" label="List of values"/>
+    </repeat>
     <expand macro="export_mtx_params"/>
   </inputs>
 
@@ -57,7 +65,7 @@
         <param name="max" value="1e9"/>
       </repeat>
       <repeat name="parameters">
-        <param name="name" value="n_counts"/>
+        <param name="name" value="gene:n_counts"/>
         <param name="min" value="0"/>
         <param name="max" value="1e9"/>
       </repeat>