changeset 6:f5ebfe244c14 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit d52bedbcef249117567014584058429525883ef7-dirty

--- a/scanpy-filter-genes.xml.bak	Tue Nov 26 05:54:31 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,94 +0,0 @@
-<?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-run-diffmap.xml	Tue Nov 26 05:54:31 2019 -0500
+++ b/scanpy-run-diffmap.xml	Wed Feb 19 11:52:37 2020 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_run_diffmap" name="Scanpy DiffusionMap" version="@TOOL_VERSION@+galaxy6">
+<tool id="scanpy_run_diffmap" name="Scanpy DiffusionMap" version="@TOOL_VERSION@+galaxy8" profile="@PROFILE@">
   <description>calculate diffusion components</description>
   <macros>
     <import>scanpy_macros2.xml</import>

--- a/scanpy_macros2.xml	Tue Nov 26 05:54:31 2019 -0500
+++ b/scanpy_macros2.xml	Wed Feb 19 11:52:37 2020 -0500
@@ -1,9 +1,12 @@
 <macros>
   <token name="@TOOL_VERSION@">1.4.3</token>
   <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
+  <token name="@PROFILE@">18.01</token>
   <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
 
+1.4.3+galaxy8: Use profile 18.01 for modules.
+
 1.4.3+galaxy6: Update to scanpy-scripts 0.2.8 (running scanpy ==1.4.3) and wider compatibility with other Galaxy modules. Bug fixes in filtering and plotting improvements.
 
 1.4.3+galaxy0: Update to scanpy-scripts 0.2.5 (running scanpy ==1.4.3).