Mercurial > repos > bgruening > 10x_bamtofastq

annotate 10x_bamtofastq.xml @ 1:f71fd828c126 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 60c20816923303efe1185c76f38a5b9a6fb8ce1c
author bgruening
date Thu, 12 May 2022 16:54:20 +0000
parents 110076d77197
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
1 <tool id="10x_bamtofastq" name="Convert a 10X BAM file to FASTQ" version="1.4.1">
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
2 <requirements>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
3 <requirement type="package" version="1.4.1">10x_bamtofastq</requirement>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
4 </requirements>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
5 <command detect_errors="exit_code"><![CDATA[
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
6 bamtofastq --nthreads "\${GALAXY_SLOTS:-4}" --reads-per-fastq 10000000000
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
7 #if $convert.reads == 'subset':
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
8 --locus $convert.locus
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
9 #end if
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
10 $produced_from
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
11 $tenx_bam
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
12 outdir &&
1
f71fd828c126 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 60c20816923303efe1185c76f38a5b9a6fb8ce1c
bgruening
parents: 0
diff changeset
13 cd outdir; for i in */*.fastq.gz;do mv \$i \${i/\//_};done
0
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
14 ]]></command>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
15 <inputs>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
16 <param format="bam" name="tenx_bam" type="data" label="10X Genomics BAM file to convert to FASTQ"/>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
17 <conditional name="convert">
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
18 <param name="reads" type="select" label="Read pairs to convert?">
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
19 <option value="all">Complete BAM file</option>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
20 <option value="subset">Only a subset of BAM file</option>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
21 </param>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
22 <when value="all" />
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
23 <when value="subset">
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
24 <param name="locus" type="text" value=""
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
25 label="Only include read pairs mapping to a locus."
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
26 help="The format is chr:start-end, for example &quot;chr1:14300-125000&quot;.">
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
27 <sanitizer>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
28 <valid initial="string.letters,string.digits">
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
29 <add value=":"/>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
30 <add value="-"/>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
31 </valid>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
32 </sanitizer>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
33 </param>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
34 </when>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
35 </conditional>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
36 <param name="sort" type="boolean" label="Skip unpaired or duplicated reads instead of throwing an error?" checked="False" falsevalue="" truevalue="--relaxed"/>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
37 <param name="produced_from" type="select" label="BAM file produced from">
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
38 <option value="">Long Ranger v2.1+ and Cell Ranger v1.2+</option>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
39 <option value="--gemcode">GemCode data (Longranger 1.0 - 1.3)</option>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
40 <option value="--lr20">Longranger 2.0</option>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
41 <option value="--cr11">Cell Ranger 1.0-1.1</option>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
42 </param>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
43 </inputs>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
44 <outputs>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
45 <collection name="fastq_collection" type="list" label="10x FASTQs from ${on_string}">
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
46 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fastq\.gz" directory="outdir" format="fastqsanger.gz"/>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
47 </collection>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
48 </outputs>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
49
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
50 <tests>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
51 <test>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
52 <param name="tenx_bam" value="A10.sub.bam"/>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
53 <output_collection name="fastq_collection" type="list" count="3">
1
f71fd828c126 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 60c20816923303efe1185c76f38a5b9a6fb8ce1c
bgruening
parents: 0
diff changeset
54 <element name="A10_MissingLibrary_1_CB54YACXX_bamtofastq_S1_L007_I1_001" file="bamtofastq_S1_L007_I1_001.fastq.gz"/>
f71fd828c126 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 60c20816923303efe1185c76f38a5b9a6fb8ce1c
bgruening
parents: 0
diff changeset
55 <element name="A10_MissingLibrary_1_CB54YACXX_bamtofastq_S1_L007_R1_001" file="bamtofastq_S1_L007_R1_001.fastq.gz"/>
f71fd828c126 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 60c20816923303efe1185c76f38a5b9a6fb8ce1c
bgruening
parents: 0
diff changeset
56 <element name="A10_MissingLibrary_1_CB54YACXX_bamtofastq_S1_L007_R2_001" file="bamtofastq_S1_L007_R2_001.fastq.gz"/>
0
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
57 </output_collection>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
58 </test>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
59 </tests>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
60 <help><![CDATA[
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
61 10x Genomics BAM to FASTQ converter
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
62 ]]></help>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
63 <citations>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
64 <citation type="bibtex">
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
65 @misc{github10xbamtofastq,
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
66 author = {},
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
67 year = {2022},
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
68 title = {10x bamtofastq},
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
69 publisher = {Github},
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
70 journal = {Github repository},
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
71 url = {https://github.com/10XGenomics/bamtofastq},
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
72 }</citation>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
73 </citations>
110076d77197 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
bgruening
parents:
diff changeset
74 </tool>