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annotate picard_CleanSam.xml @ 21:6f9c0884a3e7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 78c3dea7dcd0c854fe7e6dc1d2b2349956167661
author iuc
date Tue, 16 Oct 2018 11:49:10 -0400
parents 2a17c789e0a5
children f9242e01365a
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1 <tool id="picard_CleanSam" name="CleanSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
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2 <description>perform SAM/BAM grooming</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 <token name="@WRAPPER_VERSION@">1</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 @java_options@
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10 @symlink_element_identifier@
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11 picard
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12 CleanSam
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13 INPUT='$escaped_element_identifier'
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14 OUTPUT="${outFile}"
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15 QUIET=true
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16 VERBOSITY=ERROR
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17 @TMPDIR_OPTION@
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18 VALIDATION_STRINGENCY=${validation_stringency}
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19 ]]></command>
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21 <inputs>
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22 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
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23
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24 <expand macro="VS" />
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26 </inputs>
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28 <outputs>
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29 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset">
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30 </data>
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31 </outputs>
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34 <tests>
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35 <test>
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36 <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" />
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37 <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" lines_diff="4"/>
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38 </test>
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39 </tests>
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40
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41 <help>
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42
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43 .. class:: infomark
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44
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45 **Purpose**
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46
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47 Read SAM/BAM and perform various fix-ups. Currently, the only fix-ups are:
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48
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49 1. to soft-clip an alignment that hangs off the end of its reference sequence.
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50 2. to set MAPQ to 0 if a read is unmapped.
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51
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52 @dataset_collections@
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53
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54 @more_info@
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55
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56 </help>
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57 <expand macro="citations" />
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58 </tool>