changeset 4:1b0fdf08a454 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604

--- a/scanpy-filter-cells.xml	Mon Oct 28 05:27:24 2019 -0400
+++ b/scanpy-filter-cells.xml	Wed Nov 20 05:18:49 2019 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_filter_cells" name="Scanpy FilterCells" version="@TOOL_VERSION@+galaxy1">
+<tool id="scanpy_filter_cells" name="Scanpy FilterCells" version="@TOOL_VERSION@+galaxy0">
   <description>based on counts and numbers of genes expressed</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -16,7 +16,7 @@
     ${pars}
 #end if
 #if $categories
-    #set cats = ' '.join(['--category c:{name} {values}'.format(**$c) for $c in $categories])
+    #set cats = ' '.join(["--category c:{name} '{negate}{values}'".format(**$c) for $c in $categories])
     ${cats}
 #end if
 #if $subsets
@@ -47,7 +47,8 @@
 
     <repeat name="categories" title="Categories used to filter cells" 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 to keep"/>
+      <param name="values" type="text" value="" label="Comma-separated list of categories"/>
+      <param name="negate" type="boolean" truevalue="!" falsevalue="" checked="false" label="Apply as negative filter" help="If enabled, specified categories will be removed rather than retained."/>
     </repeat>
 
     <repeat name="subsets" title="Subsets used to filter cells" min="0">

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy-filter-genes.xml.bak	Wed Nov 20 05:18:49 2019 -0500
@@ -0,0 +1,94 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy3">
+  <description>based on counts and numbers of cells expressed</description>
+  <macros>
+    <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
+#if $parameters
+    #set pars = ' '.join(['--param g:{name} {min} {max}'.format(**$p) for $p in $parameters])
+    ${pars}
+#end if
+#if $categories
+    #set cats = ' '.join(['--category g:{name} {negate}{values}'.format(**$c) for $c in $categories])
+    ${cats}
+#end if
+#if $subsets
+    #set subs = ' '.join(['--subset g:{name} {subset}'.format(**$s) for $s in $subsets])
+    ${subs}
+#end if
+    @INPUT_OPTS@
+    @OUTPUT_OPTS@
+    @EXPORT_MTX_OPTS@
+]]></command>
+
+  <inputs>
+    <expand macro="input_object_params"/>
+    <expand macro="output_object_params"/>
+
+    <repeat name="parameters" title="Parameters used to filter genes" min="1">
+      <param name="name" type="text" value="n_cells" label="Name of parameter to filter on" help="for example n_genes or n_counts">
+        <option value="n_cells">n_cells</option>
+        <option value="n_counts">n_counts</option>
+      </param>
+      <param name="min" type="float" min="0" value="0" label="Min value"/>
+      <param name="max" type="float" min="0" value="1e9" label="Max value"/>
+    </repeat>
+
+    <repeat name="categories" title="Categories used to filter genes" min="0">
+      <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
+      <param name="values" type="text" value="" label="Comma-separated list of categories"/>
+      <param name="negate" type="boolean" truevalue="!" falsevalue="" checked="false" label="Apply as negative filter" help="If enabled, specified categories will be removed rather than retained."/>
+    </repeat>
+
+    <repeat name="subsets" title="Subsets used to filter genes" min="0">
+      <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
+      <param name="subset" type="data" format="tabular" label="List of values to keep" help="A one-column headerless text file is required"/>
+    </repeat>
+    <expand macro="export_mtx_params"/>
+  </inputs>
+
+  <outputs>
+    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Filtered genes"/>
+    <expand macro="export_mtx_outputs"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input_obj_file" value="filter_cells.h5"/>
+      <param name="input_format" value="anndata"/>
+      <param name="output_format" value="anndata"/>
+      <repeat name="parameters">
+        <param name="name" value="n_cells"/>
+        <param name="min" value="3"/>
+        <param name="max" value="1e9"/>
+      </repeat>
+      <repeat name="parameters">
+        <param name="name" value="n_counts"/>
+        <param name="min" value="0"/>
+        <param name="max" value="1e9"/>
+      </repeat>
+      <output name="output_h5" file="filter_genes.h5" ftype="h5" compare="sim_size"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+=====================================================================
+Filter genes based on arbitrary attributes (`scanpy.pp.filter_genes`)
+=====================================================================
+
+Keep genes that have at least `min_counts` counts or are expressed in at
+least `min_cells` cells or have at most `max_counts` counts or are expressed
+in at most `max_cells` cells. Other gene attributes can be used for filtering
+too if available.
+
+
+@HELP@
+
+@VERSION_HISTORY@
+]]></help>
+  <expand macro="citations"/>
+</tool>

--- a/scanpy_macros2.xml	Mon Oct 28 05:27:24 2019 -0400
+++ b/scanpy_macros2.xml	Wed Nov 20 05:18:49 2019 -0500
@@ -33,7 +33,7 @@
 
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="0.2.5.post1">scanpy-scripts</requirement>
+      <requirement type="package" version="0.2.6">scanpy-scripts</requirement>
       <yield/>
     </requirements>
   </xml>