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annotate picard_SortSam.xml @ 29:1aac2a13842a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
author iuc
date Sun, 20 Mar 2022 14:06:40 +0000
parents 2a17c789e0a5
children f9242e01365a
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1 <tool id="picard_SortSam" name="SortSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
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2 <description>sort SAM/BAM dataset</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 #if $sort_order == "queryname":
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10 #set $output = "output.sam"
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11 ln -s '${outFile}' output.sam &&
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12 #else:
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13 #set $output = $outFile
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14 #end if
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15 @java_options@
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16 @symlink_element_identifier@
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17 picard
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18 SortSam
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19 INPUT='$escaped_element_identifier'
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20 OUTPUT='${output}'
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21 SORT_ORDER="${sort_order}"
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22 QUIET=true
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23 VERBOSITY=ERROR
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24 @TMPDIR_OPTION@
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25 VALIDATION_STRINGENCY=${validation_stringency}
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26 ]]></command>
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27
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28 <inputs>
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29 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
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30 <param name="sort_order" type="select" display="radio" label="Sort order" help="SORT_ORDER; default=coordinate. Selecting Queryname will output SAM file, as Galaxy does not support BAM files that are not coordinate sorted.">
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31 <option value="coordinate" selected="True">Coordinate</option>
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32 <option value="queryname">Queryname</option>
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33 </param>
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34 <expand macro="VS" />
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35 </inputs>
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36
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37 <outputs>
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38 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Alignment sorted in ${sort_order} order">
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39 <change_format>
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40 <when input="sort_order" value="queryname" format="sam"/>
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41 </change_format>
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42 </data>
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43 </outputs>
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45
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46 <tests>
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47 <!-- This test fails when setting metadata on non-coordinate sorted bam files.
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48 This should be handled better in Galaxy (info as of release 16.0).
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49 Workaroudn is to produce queryname sorted sam files.
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50 <test>
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51 <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
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52 <param name="sort_order" value="queryname"/>
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53 <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="4"/>
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54 </test>
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55 -->
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56 <test>
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57 <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
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58 <param name="sort_order" value="queryname"/>
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59 <output name="outFile" file="picard_SortSam_test1.sam" ftype="sam" lines_diff="4" compare="contains"/>
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60 </test>
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61 <test>
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62 <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
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63 <param name="sort_order" value="coordinate"/>
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64 <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="4"/>
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65 </test>
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66 </tests>
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67
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68 <help>
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69
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70 .. class:: infomark
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71
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72 **Purpose**
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73
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74 Sorts the input SAM or BAM.
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75
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76 @dataset_collections@
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77
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78 @description@
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79
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80 SORT_ORDER=SortOrder
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81 SO=SortOrder Sort order of output file. You can either sort by queryname or by coordinate.
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82
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83 @more_info@
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84
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85 </help>
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86 <expand macro="citations" />
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87 </tool>