Mercurial > repos > iuc > khmer_extract_partitions

comparison extract-partitions.xml @ 11:43ffe9695c10 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
author iuc
date Thu, 03 Oct 2024 13:45:20 +0000
parents 13e404fd854b
children
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10:13e404fd854b 11:43ffe9695c10
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"/>
4 <macros> 3 <macros>
5 <token name="@BINARY@">extract-partitions.py</token> 4 <token name="@BINARY@">extract-partitions.py</token>
6 <import>macros.xml</import> 5 <import>macros.xml</import>
7 </macros> 6 </macros>
7 <expand macro="bio_tools"/>
8 <expand macro="requirements" /> 8 <expand macro="requirements" />
9 <expand macro="stdio" /> 9 <expand macro="stdio" />
10 <expand macro="version" /> 10 <expand macro="version" />
11 <command><![CDATA[ 11 <command><![CDATA[
12 mkdir -p output && 12 mkdir -p output &&
21 #end for 21 #end for
22 ]]> 22 ]]>
23 </command> 23 </command>
24 <inputs> 24 <inputs>
25 <expand macro="input_sequences_filenames" /> 25 <expand macro="input_sequences_filenames" />
26 <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"
27 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"/>
28 <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"
29 help="The minimum partition size worth keeping (--min-partition-size/-m)" /> 29 help="The minimum partition size worth keeping (--min-partition-size/-m)" />
30 <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=""
31 label="Output unassigned sequences" help="(--output-unassigned/-U)" /> 31 label="Output unassigned sequences" help="(--output-unassigned/-U)" />
32 </inputs> 32 </inputs>
33 <outputs> 33 <outputs>
34 <data name="distribution" format="txt" from_work_dir="output.dist" label="${tool.name} on ${on_string}: Partition size distribution" /> 34 <data name="distribution" format="txt" from_work_dir="output/output.dist" label="${tool.name} on ${on_string}: Partition size distribution" />
35 <collection name="groups-of-partitions" type="list"> 35 <collection name="groups_of_partitions" type="list" format="fasta">
36 <discover_datasets pattern="__name__" directory="output" /> 36 <discover_datasets pattern="__name__" directory="output" format="fasta"/>
37 </collection> 37 </collection>
38 </outputs> 38 </outputs>
39 <tests> 39 <tests>
40 <test> 40 <test>
41 <param name="inputs" value="random-20-a.fa.part"/> 41 <param name="inputs" value="random-20-a.fa.part"/>
42 <output_collection name="groups-of-partitions"> 42 <output name="distribution">
43 <assert_contents>
44 <has_text text="99 1 1 99"/>
45 </assert_contents>
46 </output>
47 <output_collection name="groups_of_partitions">
43 <element name="output.group0000.fa" file="random-20-a.part.extract.fa" /> 48 <element name="output.group0000.fa" file="random-20-a.part.extract.fa" />
44 </output_collection> 49 </output_collection>
45 </test> 50 </test>
46 51
47 </tests> 52 </tests>