Mercurial > repos > refinery-platform > picard_merge_sam_files

annotate picard_MergeSamFiles.xml @ 7:28f273969b5e 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 10:52:59 -0500
parents 2c6b2c6ee3bb
children afcccc536c1d
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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 <requirements>
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4 <requirement type="package" version="1.126.0">picard</requirement>
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5 </requirements>
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6
0
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7 <macros>
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8 <import>picard_macros.xml</import>
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9 </macros>
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10 <command detect_errors="exit_code"><![CDATA[
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11 @java_options@
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12 #for $index, $listCollection in enumerate($inputList):
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13 &&
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14 java -jar \$JAVA_JAR_PATH/picard.jar
0
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15 MergeSamFiles
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17 #for $element in $listCollection:
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18 INPUT="${element}"
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19 #end for
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21 OUTPUT="${'merged{}.bam'.format($index)}"
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22 MERGE_SEQUENCE_DICTIONARIES="${merge_sequence_dictionaries}"
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23 ASSUME_SORTED="${assume_sorted}"
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24 #for $element in $comments:
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25 COMMENT="${element.comment}"
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26 #end for
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27 USE_THREADING=true
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28 SORT_ORDER=coordinate
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29 VALIDATION_STRINGENCY="${validation_stringency}"
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30 QUIET=true
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31 VERBOSITY=ERROR
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32 #end for
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33 ]]></command>
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34 <inputs>
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35 <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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36 <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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37 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/>
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38
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39 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
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40 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
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41 </repeat>
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43 <expand macro="VS" />
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44
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45 </inputs>
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46
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47 <outputs>
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48 <data format="bam" name="merged">
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49 <discover_datasets pattern="__designation_and_ext__" visible="true" />
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50 </data>
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51 </outputs>
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52
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53 <tests>
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54 <test>
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55 <param name="inputList">
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56 <collection type="list:list">
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57 <element name="list 1">
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58 <collection type="list">
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59 <element name="l1_input1" value="picard_MergeSamFiles_input1.bam" />
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60 <element name="l1_input2" value="picard_MergeSamFiles_input2.bam" />
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61 <element name="l1_input3" value="picard_MergeSamFiles_input3.bam" />
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62 </collection>
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63 </element>
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64 <element name="list 2">
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65 <collection type="list">
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66 <element name="l2_input1" value="picard_MergeSamFiles_input1.bam" />
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67 <element name="l2_input2" value="picard_MergeSamFiles_input2.bam" />
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68 <element name="l2_input3" value="picard_MergeSamFiles_input3.bam" />
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69 </collection>
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70 </element>
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71 </collection>
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72 </param>
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73 <param name="assume_sorted" value="False"/>
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74 <param name="merge_sequence_dictionaries" value="False"/>
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75 <param name="validation_stringency" value="LENIENT"/>
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76 <output name="merged0" ftype="bam">
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77 <assert_contents>
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78 <has_text text=""/>
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79 </assert_contents>
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80 </output>
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81 <output name="merged1" ftype="bam">
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82 <assert_contents>
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83 <has_text text=""/>
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84 </assert_contents>
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85 </output>
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86 </test>
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87 </tests>
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88
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89 <stdio>
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90 <exit_code range="1:" level="fatal"/>
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91 </stdio>
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92
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93 <help>
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94
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95 **Purpose**
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96
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97 Merges multiple SAM/BAM datasets into one.
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98
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99 @dataset_collections@
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100
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101 @description@
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102
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103 ASSUME_SORTED=Boolean
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104 AS=Boolean If true, assume that the input files are in the same sort order as the requested output
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105 sort order, even if their headers say otherwise. Default value: false. This option can
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106 be set to 'null' to clear the default value. Possible values: {true, false}
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107
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108 MERGE_SEQUENCE_DICTIONARIES=Boolean
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109 MSD=Boolean Merge the sequence dictionaries Default value: false. This option can be set to 'null'
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110 to clear the default value. Possible values: {true, false}
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111
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112 COMMENT=String
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113 CO=String Comment(s) to include in the merged output file's header. This option may be specified 0
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114 or more times.
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115
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116
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117 @more_info@
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118
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119 </help>
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120 </tool>