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comparison 10x_bamtofastq.xml @ 0:110076d77197 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
author bgruening
date Tue, 10 May 2022 12:02:15 +0000
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children f71fd828c126
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-1:000000000000 0:110076d77197
1 <tool id="10x_bamtofastq" name="Convert a 10X BAM file to FASTQ" version="1.4.1">
2 <requirements>
3 <requirement type="package" version="1.4.1">10x_bamtofastq</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 bamtofastq --nthreads "\${GALAXY_SLOTS:-4}" --reads-per-fastq 10000000000
7 #if $convert.reads == 'subset':
8 --locus $convert.locus
9 #end if
10 $produced_from
11 $tenx_bam
12 outdir &&
13 mv outdir/*/*.fastq.gz outdir
14 ]]></command>
15 <inputs>
16 <param format="bam" name="tenx_bam" type="data" label="10X Genomics BAM file to convert to FASTQ"/>
17 <conditional name="convert">
18 <param name="reads" type="select" label="Read pairs to convert?">
19 <option value="all">Complete BAM file</option>
20 <option value="subset">Only a subset of BAM file</option>
21 </param>
22 <when value="all" />
23 <when value="subset">
24 <param name="locus" type="text" value=""
25 label="Only include read pairs mapping to a locus."
26 help="The format is chr:start-end, for example &quot;chr1:14300-125000&quot;.">
27 <sanitizer>
28 <valid initial="string.letters,string.digits">
29 <add value=":"/>
30 <add value="-"/>
31 </valid>
32 </sanitizer>
33 </param>
34 </when>
35 </conditional>
36 <param name="sort" type="boolean" label="Skip unpaired or duplicated reads instead of throwing an error?" checked="False" falsevalue="" truevalue="--relaxed"/>
37 <param name="produced_from" type="select" label="BAM file produced from">
38 <option value="">Long Ranger v2.1+ and Cell Ranger v1.2+</option>
39 <option value="--gemcode">GemCode data (Longranger 1.0 - 1.3)</option>
40 <option value="--lr20">Longranger 2.0</option>
41 <option value="--cr11">Cell Ranger 1.0-1.1</option>
42 </param>
43 </inputs>
44 <outputs>
45 <collection name="fastq_collection" type="list" label="10x FASTQs from ${on_string}">
46 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fastq\.gz" directory="outdir" format="fastqsanger.gz"/>
47 </collection>
48 </outputs>
49
50 <tests>
51 <test>
52 <param name="tenx_bam" value="A10.sub.bam"/>
53 <output_collection name="fastq_collection" type="list" count="3">
54 <element name="bamtofastq_S1_L007_I1_001" file="bamtofastq_S1_L007_I1_001.fastq.gz"/>
55 <element name="bamtofastq_S1_L007_R1_001" file="bamtofastq_S1_L007_R1_001.fastq.gz"/>
56 <element name="bamtofastq_S1_L007_R2_001" file="bamtofastq_S1_L007_R2_001.fastq.gz"/>
57 </output_collection>
58 </test>
59 </tests>
60 <help><![CDATA[
61 10x Genomics BAM to FASTQ converter
62 ]]></help>
63 <citations>
64 <citation type="bibtex">
65 @misc{github10xbamtofastq,
66 author = {},
67 year = {2022},
68 title = {10x bamtofastq},
69 publisher = {Github},
70 journal = {Github repository},
71 url = {https://github.com/10XGenomics/bamtofastq},
72 }</citation>
73 </citations>
74 </tool>