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annotate samtools_split_by_chrom.xml @ 0:a30dd3c77b30 draft

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author jjohnson
date Wed, 30 Nov 2016 16:46:40 -0500
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1 <tool id="samtools_split_by_chrom" name="Split BAM by Chromosome" version="2.0">
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2 <description>into collection</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <!-- <code file="samtools_slice_options.py"/> -->
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7 <expand macro="requirements"></expand>
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8 <expand macro="stdio"></expand>
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9 <expand macro="version_command"></expand>
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10 <command>
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11 <![CDATA[
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12 mkdir -p outputs &&
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13 ln -s "${input_bam}" temp_input.bam &&
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14 ln -s "${input_bam.metadata.bam_index}" temp_input.bam.bai
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15 #for $ref in str( $refs ).split(","):
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16 && samtools view -@ \${GALAXY_SLOTS:-1} -bh inputs/temp_input.bam ${ref} |
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17 samtools sort -O bam -T sorted -@ \${GALAXY_SLOTS:-1} -o "outputs/${input_bam.name}.${ref}.bam" -
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18 #end for
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param name="input_bam" format="bam" label="Select BAM dataset to slice" type="data" />
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23 <param name="refs" type="select" optional="False" multiple="True" label="Select references (chromosomes and contigs) you would like to restrict bam to" help="Click and type in the box above to see options. You can select multiple entries. If &quot;No options available&quot; is displayed, you need to re-detect metadata on the input dataset. See help section below.">
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24 <!-- The options tagset below extracts reference names from bam file metadata -->
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25 <!-- This will not work with bed files with old style metadata. However this -->
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26 <!-- Can be easily fixed by re-deceting metadata on a bam dataset by clicking -->
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27 <!-- The pencil icon and settind datatype to "bam" -->
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28 <!-- This change has been commited in the following pull request: -->
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29 <!-- https://github.com/galaxyproject/galaxy/pull/107 -->
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30 <options>
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31 <filter type="data_meta" ref="input_bam" key="reference_names" />
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32 </options>
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33 </param>
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34 </inputs>
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35 <outputs>
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36 <collection name="output_collection" type='list' label="${input_bam.name} by chrom">
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37 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.bam" directory="outputs" ext='bam'/>
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38 </collection>
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param ftype="bam" name="input_bam" value="bam-slice-input.bam" />
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43 <param name="refs" value="chrM" />
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44 <output file="bam-slice-test2.bam" ftype="bam" name="output_bam" />
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45 </test>
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46 </tests>
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47 <help>
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48 <![CDATA[
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49
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50 **What it does**
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51
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52 Creates a dataset collection of BAM files, one per selected chromosome.
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53
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54 This tool is based on ``samtools view`` command.
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55
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56 @no-chrom-options@
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57
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58 ]]>
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59 </help>
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60 <expand macro="citations"></expand>
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61 </tool>