Mercurial > repos > iuc > khmer_filter_below_abundance_cutoff

diff filter-below-abund.xml @ 7:569001af897d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
author iuc
date Wed, 18 Dec 2019 16:01:57 -0500
parents bf716cfc3225
children b469ab47b490
line wrap: on
line diff
--- a/filter-below-abund.xml	Fri Sep 07 11:01:54 2018 -0400
+++ b/filter-below-abund.xml	Wed Dec 18 16:01:57 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="khmer_filter_below_abundance_cutoff" name="Filter reads" version="@WRAPPER_VERSION@.0">
+<tool id="khmer_filter_below_abundance_cutoff" name="khmer: Filter reads" version="@WRAPPER_VERSION@@TOOL_VERSION@">
     <description>
         below k-mer abundance of 50
     </description>
@@ -6,36 +6,34 @@
         <token name="@BINARY@">filter-below-abund.py</token>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="requirements">
+        <requirement type="package" version="1.0.1">screed</requirement>
+    </expand>
     <expand macro="stdio" />
     <command><![CDATA[
-        #for $num, $input in enumerate($inputs)
-            ln -s '${input}' sequence-${num} &&
-        #end for
-        mkdir output &&
-        cd output &&
-        python '$__tool_directory__/@BINARY@'
-        '${input_countgraph_filename}'
-        #for $num, $input in enumerate($inputs)
-           ../sequence-${num}
-        #end for
-    ]]>
+@LINK_SEQUENCES@   
+mkdir output &&
+cd output &&
+python '$__tool_directory__/@BINARY@'
+'${input_countgraph_filename}'
+@USE_SEQUENCES@
+> '$log'
+]]>
     </command>
     <inputs>
         <expand macro="input_sequences_filenames" />
         <expand macro="input_countgraph_filename" />
     </inputs>
     <outputs>
-        <collection name="sequence_files" type="list">
-            <discover_datasets pattern="__name__" directory="output" />
-        </collection>
+        <data name="log" format="txt" />
+        <expand macro="output_sequences" extension="below"/>
     </outputs>
     <tests>
         <test>
             <param name="inputs" value="test-abund-read-2.fa" />
             <param name="input_countgraph_filename" value="test-abund-read-2.large.oxlicg" ftype="oxlicg" />
-            <output_collection name="sequence_files">
-                <element name="sequence-0.below" file="test-abund-read-2.fa.below" />
+            <output_collection name="sequences">
+                <element name="test-abund-read-2.fa" file="test-abund-read-2.fa.below" />
             </output_collection>
         </test>
     </tests>