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comparison picard_CollectRnaSeqMetrics.xml @ 12:05087b27692a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author devteam
date Sun, 27 Nov 2016 15:11:50 -0500
parents 5eaa8a968300
children 7e6fd3d0f16e
comparison
equal deleted inserted replaced
11:efc56ee1ade4 12:05087b27692a
2 <description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</description> 2 <description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
7 <requirement type="package" version="3.1.2">R</requirement> 7 <requirement type="package" version="3.3.1">r</requirement>
8 </expand> 8 </expand>
9 <command> 9 <command detect_errors="exit_code"><![CDATA[
10 10
11 ## Set up input files 11 ## Set up input files
12 12
13 ## Reference sequences 13 ## Reference sequences
14 14
15 #set $reference_fasta_filename = "localref.fa" 15 #set $reference_fasta_filename = "localref.fa"
16 16
17 #if str( $reference_source.reference_source_selector ) == "history": 17 #if str( $reference_source.reference_source_selector ) == "history":
18 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp; 18 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
19 #else: 19 #else:
20 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 20 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
21 #end if 21 #end if
22 22
23 ## refFlat data 23 ## refFlat data
24 ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format 24 ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format
25 25
26 grep -v '^#' ${refFlat} | awk '{print $11"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > refFlat.tab &amp;&amp; 26 grep -v '^#' ${refFlat} | awk '{print $11"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > refFlat.tab &&
27 27
28 ## Start picard command 28 ## Start picard command
29 29
30 @java_options@ 30 @java_options@
31 java -jar \$JAVA_JAR_PATH/picard.jar 31 picard
32 CollectRnaSeqMetrics 32 CollectRnaSeqMetrics
33 REF_FLAT=refFlat.tab 33 REF_FLAT=refFlat.tab
34 34
35 #if str( $ribosomal_intervals ) != "None": 35 #if str( $ribosomal_intervals ) != "None":
36 RIBOSOMAL_INTERVALS="${ribosomal_intervals}" 36 RIBOSOMAL_INTERVALS="${ribosomal_intervals}"
53 53
54 QUIET=true 54 QUIET=true
55 VERBOSITY=ERROR 55 VERBOSITY=ERROR
56 VALIDATION_STRINGENCY=${validation_stringency} 56 VALIDATION_STRINGENCY=${validation_stringency}
57 57
58 </command> 58 ]]></command>
59 59
60 <inputs> 60 <inputs>
61 <param format="sam,bam" type="data" name="inputFile" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> 61 <param format="sam,bam" type="data" name="inputFile" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
62 <conditional name="reference_source"> 62 <conditional name="reference_source">
63 <param name="reference_source_selector" type="select" label="Load reference genome from"> 63 <param name="reference_source_selector" type="select" label="Load reference genome from">
75 </when> 75 </when>
76 </conditional> 76 </conditional>
77 <param format="tabular" name="refFlat" type="data" label="Gene annotations in refFlat form" help="See &quot;Obtaining gene annotations in refFlat format&quot; below for help" /> 77 <param format="tabular" name="refFlat" type="data" label="Gene annotations in refFlat form" help="See &quot;Obtaining gene annotations in refFlat format&quot; below for help" />
78 <param name="ribosomal_intervals" format="picard_interval_list" type="data" optional="True" label="Location of rRNA sequences in genome, in interval_list format" help="RIBOSOMAL_INTERVALS; If not specified no bases will be identified as being ribosomal. The list of intervals can be geberated from BED or Interval datasets using Galaxy BedToIntervalList tool"/> 78 <param name="ribosomal_intervals" format="picard_interval_list" type="data" optional="True" label="Location of rRNA sequences in genome, in interval_list format" help="RIBOSOMAL_INTERVALS; If not specified no bases will be identified as being ribosomal. The list of intervals can be geberated from BED or Interval datasets using Galaxy BedToIntervalList tool"/>
79 <param name="strand_specificity" type="select" label="What is the RNA-seq library strand specificity" help="STRAND_SPECIFICITY; For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand."> 79 <param name="strand_specificity" type="select" label="What is the RNA-seq library strand specificity" help="STRAND_SPECIFICITY; For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand.">
80 <option value="NONE" select="True">None</option> 80 <option value="NONE" selected="True">None</option>
81 <option value="FIRST_READ_TRANSCRIPTION_STRAND">First read transcription strand</option> 81 <option value="FIRST_READ_TRANSCRIPTION_STRAND">First read transcription strand</option>
82 <option value="SECOND_READ_TRANSCRIPTION_STRAND">Second read transcription strand</option> 82 <option value="SECOND_READ_TRANSCRIPTION_STRAND">Second read transcription strand</option>
83 </param> 83 </param>
84 <param name="minimum_length" type="integer" value="500" label="When calculating coverage based values use only use transcripts of this length or greater" help="MINIMUM_LENGTH; default=500"/> 84 <param name="minimum_length" type="integer" value="500" label="When calculating coverage based values use only use transcripts of this length or greater" help="MINIMUM_LENGTH; default=500"/>
85 <repeat name="ignore_list" title="Sequences to ignore" min="0" help="You can provide multiple sequences by clicking the button below"> 85 <repeat name="ignore_list" title="Sequences to ignore" min="0" help="You can provide multiple sequences by clicking the button below">
100 <outputs> 100 <outputs>
101 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> 101 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
102 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> 102 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
103 </outputs> 103 </outputs>
104 104
105 <stdio>
106 <exit_code range="1:" level="fatal"/>
107 </stdio>
108 <tests> 105 <tests>
109 <test> 106 <test>
110 <param name="reference_source_selector" value="history"/> 107 <param name="reference_source_selector" value="history"/>
111 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> 108 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
112 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> 109 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>