Mercurial > repos > bgruening > 10x_bamtofastq

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