Mercurial > repos > iuc > khmer_extract_partitions

comparison extract-partitions.xml @ 8:adb3dd5a899f draft default tip

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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
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7:98b53d46e851 8:adb3dd5a899f
1 <tool id="khmer_extract_partitions" name="khmer: Extract partitions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="khmer_extract_partitions" name="khmer: Extract partitions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Separate sequences that are annotated with partitions into grouped files</description> 2 <description>Separate sequences that are annotated with partitions into grouped files</description>
3 <expand macro="bio_tools"/>
3 <macros> 4 <macros>
4 <token name="@BINARY@">extract-partitions.py</token> 5 <token name="@BINARY@">extract-partitions.py</token>
5 <import>macros.xml</import> 6 <import>macros.xml</import>
6 </macros> 7 </macros>
7 <expand macro="requirements" /> 8 <expand macro="requirements" />
20 #end for 21 #end for
21 ]]> 22 ]]>
22 </command> 23 </command>
23 <inputs> 24 <inputs>
24 <expand macro="input_sequences_filenames" /> 25 <expand macro="input_sequences_filenames" />
25 <param argument="--max-size" name="max_size" type="integer" label="Max group size" value="1000000" 26 <param argument="--max-size" type="integer" label="Max group size" value="1000000"
26 help="No more than this many number of sequences will be stored in each output"/> 27 help="No more than this many number of sequences will be stored in each output"/>
27 <param name="min_partition_size" type="integer" label="Min partition size" value="5" 28 <param name="min_partition_size" type="integer" label="Min partition size" value="5"
28 help="The minimum partition size worth keeping (--min-partition-size/-m)" /> 29 help="The minimum partition size worth keeping (--min-partition-size/-m)" />
29 <param name="output_unassigned" type="boolean" checked="false" truevalue="--output-unassigned" falsevalue="" 30 <param name="output_unassigned" type="boolean" checked="false" truevalue="--output-unassigned" falsevalue=""
30 label="Output unassigned sequences" help="(--output-unassigned/-U)" /> 31 label="Output unassigned sequences" help="(--output-unassigned/-U)" />
31 </inputs> 32 </inputs>
32 <outputs> 33 <outputs>
33 <data name="distribution" format="txt" from_work_dir="output.dist" label="${tool.name} on ${on_string}: Partition size distribution" /> 34 <data name="distribution" format="txt" from_work_dir="output.dist" label="${tool.name} on ${on_string}: Partition size distribution" />
34 <collection name="groups-of-partitions" type="list"> 35 <collection name="groups-of-partitions" type="list" format="fasta">
35 <discover_datasets pattern="__name__" directory="output" /> 36 <discover_datasets pattern="__name__" directory="output" format="fasta"/>
36 </collection> 37 </collection>
37 </outputs> 38 </outputs>
38 <tests> 39 <tests>
39 <test> 40 <test>
40 <param name="inputs" value="random-20-a.fa.part"/> 41 <param name="inputs" value="random-20-a.fa.part"/>