Mercurial > repos > refinery-platform > picard_merge_sam_files

annotate picard_MergeSamFiles.xml @ 4:2c6b2c6ee3bb draft

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planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 2137a21daebbb1cf755e8bf99fae7f5a77b07f87-dirty
author refinery-platform
date Mon, 04 Dec 2017 10:16:33 -0500
parents 40d9376df6d6
children 28f273969b5e
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1 <tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.0">
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2 <description>merges multiple SAM/BAM datasets into one</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 </macros>
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6 <command detect_errors="exit_code"><![CDATA[
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7 @java_options@
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8 #for $index, $listCollection in enumerate($inputList):
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9 &&
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10 java -jar \$JAVA_JAR_PATH/picard.jar
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11 MergeSamFiles
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12
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13 #for $element in $listCollection:
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14 INPUT="${element}"
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15 #end for
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16
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17 OUTPUT="${'merged{}.bam'.format($index)}"
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18 MERGE_SEQUENCE_DICTIONARIES="${merge_sequence_dictionaries}"
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19 ASSUME_SORTED="${assume_sorted}"
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20 #for $element in $comments:
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21 COMMENT="${element.comment}"
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22 #end for
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23 USE_THREADING=true
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24 SORT_ORDER=coordinate
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25 VALIDATION_STRINGENCY="${validation_stringency}"
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26 QUIET=true
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27 VERBOSITY=ERROR
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28 #end for
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29 ]]></command>
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30 <inputs>
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31 <param format="sam,bam" name="inputList" type="data_collection" collection_type="list:list" label="Select SAM/BAM dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
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32 <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/>
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33 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/>
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34
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35 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
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36 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
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37 </repeat>
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38
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39 <expand macro="VS" />
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40
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41 </inputs>
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42
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43 <outputs>
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44 <data format="bam" name="merged">
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45 <discover_datasets pattern="__designation_and_ext__" visible="true" />
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46 </data>
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47 </outputs>
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48
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49 <tests>
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50 <test>
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51 <param name="inputList">
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52 <collection type="list:list">
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53 <element name="list 1">
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54 <collection type="list">
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55 <element name="l1_input1" value="picard_MergeSamFiles_input1.bam" />
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56 <element name="l1_input2" value="picard_MergeSamFiles_input2.bam" />
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57 <element name="l1_input3" value="picard_MergeSamFiles_input3.bam" />
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58 </collection>
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59 </element>
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60 <element name="list 2">
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61 <collection type="list">
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62 <element name="l2_input1" value="picard_MergeSamFiles_input1.bam" />
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63 <element name="l2_input2" value="picard_MergeSamFiles_input2.bam" />
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64 <element name="l2_input3" value="picard_MergeSamFiles_input3.bam" />
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65 </collection>
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66 </element>
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67 </collection>
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68 </param>
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69 <param name="assume_sorted" value="False"/>
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70 <param name="merge_sequence_dictionaries" value="False"/>
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71 <param name="validation_stringency" value="LENIENT"/>
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72 <output name="merged0" ftype="bam">
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73 <assert_contents>
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74 <has_text text=""/>
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75 </assert_contents>
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76 </output>
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77 <output name="merged1" ftype="bam">
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78 <assert_contents>
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79 <has_text text=""/>
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80 </assert_contents>
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81 </output>
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82 </test>
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83 </tests>
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84
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85 <stdio>
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86 <exit_code range="1:" level="fatal"/>
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87 </stdio>
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88
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89 <help>
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90
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91 **Purpose**
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92
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93 Merges multiple SAM/BAM datasets into one.
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94
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95 @dataset_collections@
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96
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97 @description@
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98
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99 ASSUME_SORTED=Boolean
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100 AS=Boolean If true, assume that the input files are in the same sort order as the requested output
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101 sort order, even if their headers say otherwise. Default value: false. This option can
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102 be set to 'null' to clear the default value. Possible values: {true, false}
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103
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104 MERGE_SEQUENCE_DICTIONARIES=Boolean
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105 MSD=Boolean Merge the sequence dictionaries Default value: false. This option can be set to 'null'
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106 to clear the default value. Possible values: {true, false}
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107
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108 COMMENT=String
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109 CO=String Comment(s) to include in the merged output file's header. This option may be specified 0
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110 or more times.
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111
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112
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113 @more_info@
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114
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115 </help>
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116 </tool>