Mercurial > repos > refinery-platform > picard_merge_sam_files

annotate picard_MergeSamFiles.xml @ 0:40d9376df6d6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
author refinery-platform
date Mon, 04 Dec 2017 09:23:06 -0500
parents
children 2c6b2c6ee3bb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
1 <tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.0">
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
2 <description>merges multiple SAM/BAM datasets into one</description>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
3 <macros>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
4 <import>picard_macros.xml</import>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
5 </macros>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
6 <expand macro="requirements" />
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
8 @java_options@
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
9 #for $index, $listCollection in enumerate($inputList):
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
10 &&
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
11 picard
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
12 MergeSamFiles
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
13
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
14 #for $element in $listCollection:
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
15 INPUT="${element}"
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
16 #end for
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
17
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
18 OUTPUT="${'merged{}.bam'.format($index)}"
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
19 MERGE_SEQUENCE_DICTIONARIES="${merge_sequence_dictionaries}"
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
20 ASSUME_SORTED="${assume_sorted}"
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
21 #for $element in $comments:
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
22 COMMENT="${element.comment}"
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
23 #end for
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
24 USE_THREADING=true
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
25 SORT_ORDER=coordinate
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
26 VALIDATION_STRINGENCY="${validation_stringency}"
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
27 QUIET=true
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
28 VERBOSITY=ERROR
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
29 #end for
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
30 ]]></command>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
31 <inputs>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
32 <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"/>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
33 <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
34 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
35
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
36 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
37 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
38 </repeat>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
39
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
40 <expand macro="VS" />
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
41
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
42 </inputs>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
43
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
44 <outputs>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
45 <data format="bam" name="merged">
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
46 <discover_datasets pattern="__designation_and_ext__" visible="true" />
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
47 </data>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
48 </outputs>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
49
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
50 <tests>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
51 <test>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
52 <param name="inputList">
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
53 <collection type="list:list">
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
54 <element name="list 1">
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
55 <collection type="list">
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
56 <element name="l1_input1" value="picard_MergeSamFiles_input1.bam" />
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
57 <element name="l1_input2" value="picard_MergeSamFiles_input2.bam" />
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
58 <element name="l1_input3" value="picard_MergeSamFiles_input3.bam" />
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
59 </collection>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
60 </element>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
61 <element name="list 2">
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
62 <collection type="list">
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
63 <element name="l2_input1" value="picard_MergeSamFiles_input1.bam" />
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
64 <element name="l2_input2" value="picard_MergeSamFiles_input2.bam" />
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
65 <element name="l2_input3" value="picard_MergeSamFiles_input3.bam" />
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
66 </collection>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
67 </element>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
68 </collection>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
69 </param>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
70 <param name="assume_sorted" value="False"/>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
71 <param name="merge_sequence_dictionaries" value="False"/>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
72 <param name="validation_stringency" value="LENIENT"/>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
73 <output name="merged0" ftype="bam">
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
74 <assert_contents>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
75 <has_text text=""/>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
76 </assert_contents>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
77 </output>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
78 <output name="merged1" ftype="bam">
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
79 <assert_contents>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
80 <has_text text=""/>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
81 </assert_contents>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
82 </output>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
83 </test>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
84 </tests>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
85
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
86 <stdio>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
87 <exit_code range="1:" level="fatal"/>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
88 </stdio>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
89
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
90 <help>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
91
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
92 **Purpose**
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
93
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
94 Merges multiple SAM/BAM datasets into one.
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
95
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
96 @dataset_collections@
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
97
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
98 @description@
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
99
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
100 ASSUME_SORTED=Boolean
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
101 AS=Boolean If true, assume that the input files are in the same sort order as the requested output
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
102 sort order, even if their headers say otherwise. Default value: false. This option can
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
103 be set to 'null' to clear the default value. Possible values: {true, false}
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
104
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
105 MERGE_SEQUENCE_DICTIONARIES=Boolean
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
106 MSD=Boolean Merge the sequence dictionaries Default value: false. This option can be set to 'null'
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
107 to clear the default value. Possible values: {true, false}
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
108
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
109 COMMENT=String
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
110 CO=String Comment(s) to include in the merged output file's header. This option may be specified 0
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
111 or more times.
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
112
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
113
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
114 @more_info@
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
115
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
116 </help>
40d9376df6d6 planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty
refinery-platform
parents:
diff changeset
117 </tool>