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comparison bam_to_bigwig.xml @ 5:5b40b93ebae3 default tip

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Added advanced settings
author Lance Parsons <lparsons@princeton.edu>
date Wed, 24 Aug 2011 16:44:28 -0400
parents b8525303b945
children
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4:3112c78841c5 5:5b40b93ebae3
6 </requirements> 6 </requirements>
7 <command> 7 <command>
8 genomeCoverageBed -ibam $align -bg $split -g 8 genomeCoverageBed -ibam $align -bg $split -g
9 `awk '($0 !~ /^#.*/) &amp;&amp; ($2 == "$align.dbkey") {print $3}' ${GALAXY_DATA_INDEX_DIR}/sam_fa_indices.loc`.fai 9 `awk '($0 !~ /^#.*/) &amp;&amp; ($2 == "$align.dbkey") {print $3}' ${GALAXY_DATA_INDEX_DIR}/sam_fa_indices.loc`.fai
10 > tmp.bedgraph; 10 > tmp.bedgraph;
11 bedGraphToBigWig tmp.bedgraph 11 bedGraphToBigWig
12 #if $settings.settingsType == "full":
13 -blockSize=${settings.blockSize} -itemsPerSlot=${settings.itemsPerSlot} ${settings.unc}
14 #end if
15 tmp.bedgraph
12 `awk '($0 !~ /^#.*/) &amp;&amp; ($2 == "$align.dbkey") {print $3}' ${GALAXY_DATA_INDEX_DIR}/sam_fa_indices.loc`.fai 16 `awk '($0 !~ /^#.*/) &amp;&amp; ($2 == "$align.dbkey") {print $3}' ${GALAXY_DATA_INDEX_DIR}/sam_fa_indices.loc`.fai
13 $out; 17 $out;
14 </command> 18 </command>
15 <inputs> 19 <inputs>
16 <param name="align" type="data" format="bam" label="Select the BAM file to generate the pileup file for"> 20 <param name="align" type="data" format="bam" label="Select the BAM file to generate the pileup file for">
17 <validator type="unspecified_build" /> 21 <validator type="unspecified_build" />
18 <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" /> 22 <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" />
19 </param> 23 </param>
20 <param name="split" type="boolean" value="false" label="Separate split reads" help="Do not use gaps when computing coverage. This is recommended for RNA-Seq where reads are mapped across long splice junctions. Uses the CIGAR &quot;N&quot; and &quot;D&quot; operations to infer the blocks for computing coverage." truevalue="-split" falsevalue="" /> 24 <param name="split" type="boolean" value="false" label="Separate split reads" help="Do not use gaps when computing coverage. This is recommended for RNA-Seq where reads are mapped across long splice junctions. Uses the CIGAR &quot;N&quot; and &quot;D&quot; operations to infer the blocks for computing coverage." truevalue="-split" falsevalue="" />
25 <conditional name="settings">
26 <param name="settingsType" type="select" label="Converter settings to use" help="Default settings should usually be used.">
27 <option value="preset">Default</option>
28 <option value="full">Full parameter list</option>
29 </param>
30 <when value="preset" />
31 <when value="full">
32 <param name="blockSize" size="4" type="integer" value="256" label="Items to bundle in r-tree" help="Default is 256 (blockSize)" />
33 <param name="itemsPerSlot" size="4" type="integer" value="1024" label="Data points bundled at lowest level" help="Default is 1024 (itemsPerSlot)" />
34 <param name="unc" type="boolean" truevalue="-unc" falsevalue="" checked="False" label="Do not use compression" help="(unc)"/>
35 </when>
36 </conditional>
37
21 </inputs> 38 </inputs>
22 <outputs> 39 <outputs>
23 <data format="bigwig" name="out" /> 40 <data format="bigwig" name="out" />
24 </outputs> 41 </outputs>
25 42