Mercurial > repos > iuc > khmer_extract_partitions

changeset 8:adb3dd5a899f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author iuc
date Mon, 17 Jun 2024 11:46:55 +0000
parents 98b53d46e851
children 1061711538c6
files extract-partitions.xml macros.xml
diffstat 2 files changed, 9 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/extract-partitions.xml	Tue Mar 23 21:30:56 2021 +0000
+++ b/extract-partitions.xml	Mon Jun 17 11:46:55 2024 +0000
@@ -1,5 +1,6 @@
 <tool id="khmer_extract_partitions" name="khmer: Extract partitions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Separate sequences that are annotated with partitions into grouped files</description>
+    <expand macro="bio_tools"/>
     <macros>
         <token name="@BINARY@">extract-partitions.py</token>
         <import>macros.xml</import>
@@ -22,7 +23,7 @@
     </command>
     <inputs>
         <expand macro="input_sequences_filenames" />
-        <param argument="--max-size" name="max_size" type="integer" label="Max group size" value="1000000"
+        <param argument="--max-size" type="integer" label="Max group size" value="1000000"
             help="No more than this many number of sequences will be stored in each output"/>
         <param name="min_partition_size" type="integer" label="Min partition size" value="5"
             help="The minimum partition size worth keeping (--min-partition-size/-m)" />
@@ -31,8 +32,8 @@
     </inputs>
     <outputs>
         <data name="distribution" format="txt" from_work_dir="output.dist" label="${tool.name} on ${on_string}: Partition size distribution" />
-        <collection name="groups-of-partitions" type="list">
-            <discover_datasets pattern="__name__" directory="output" />
+        <collection name="groups-of-partitions" type="list" format="fasta">
+            <discover_datasets pattern="__name__" directory="output" format="fasta"/>
         </collection>
     </outputs>
     <tests>
--- a/macros.xml	Tue Mar 23 21:30:56 2021 +0000
+++ b/macros.xml	Mon Jun 17 11:46:55 2024 +0000
@@ -2,6 +2,11 @@
     <token name="@TOOL_VERSION@">3.0.0a3</token>
     <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">20.01</token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">khmer</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">khmer</requirement>