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comparison picard_SamToFastq.xml @ 21:1181366ba593 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit cbe534af56ee782e8d1aa0fa872059d2a5e42db8"
author iuc
date Mon, 17 Feb 2020 15:23:48 +0000
parents a5a13ea16d17
children 4740a2548206
comparison
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20:c1aaa5a116d0 21:1181366ba593
1 <tool name="SamToFastq" id="picard_SamToFastq" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="SamToFastq" id="picard_SamToFastq" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
2 <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description> 2 <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 <token name="@WRAPPER_VERSION@">1</token> 5 <token name="@WRAPPER_VERSION@">2</token>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 9
10 echo "BAM" > $report && ## This is necessary for output dataset detection (see output tags below)
11
12 @java_options@ 10 @java_options@
13 @symlink_element_identifier@ 11 @symlink_element_identifier@
14 12
15 picard 13 picard
16 SamToFastq 14 SamToFastq
17 15
18 INPUT='$escaped_element_identifier' 16 INPUT='$escaped_element_identifier'
19 17
20 #if str( $output_per_rg ) == "true": 18 #if str($single_or_paired) == "pe_interleaved":
21 OUTPUT_PER_RG=true 19 FASTQ='${interleaved_fastq}'
22 OUTPUT_DIR=. 20 INTERLEAVE=TRUE
23 #elif str( $output_per_rg ) == "false" and str( $interleave ) == "false": 21 #else if str($single_or_paired) == "pe_sep":
24 FASTQ=READ1.fastq 22 F='${fq1}'
25 SECOND_END_FASTQ=READ2.fastq 23 F2='${fq2}'
26 UNPAIRED_FASTQ=UNPAIRED_READS.fastq 24 FU='${fq_u}'
27 #elif str( $output_per_rg ) == "false" and str( $interleave ) == "true": 25 #else
28 FASTQ=INTERLEAVED.fastq 26 F='${fq_single}'
29 #end if 27 #end if
30 28
31 RE_REVERSE="${re_reverse}" 29 RE_REVERSE="${re_reverse}"
32 INTERLEAVE="${interleave}" 30
33 INCLUDE_NON_PF_READS="${include_non_pf_reads}" 31 INCLUDE_NON_PF_READS="${include_non_pf_reads}"
34 CLIPPING_ATTRIBUTE="${clipping_attribute}" 32 #if len(str($clipping_attribute)) > 0:
35 CLIPPING_ACTION="${clipping_action}" 33 CLIPPING_ATTRIBUTE="${clipping_attribute}"
34 #end if
35 #if len(str($clipping_action)) > 0:
36 CLIPPING_ACTION="${clipping_action}"
37 #end if
36 READ1_TRIM="${read1_trim}" 38 READ1_TRIM="${read1_trim}"
37 39
38 #if int($read1_max_bases_to_write) > -1: 40 #if int($read1_max_bases_to_write) > -1:
39 READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}" 41 READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}"
40 #end if 42 #end if
44 #if int($read2_max_bases_to_write) > -1: 46 #if int($read2_max_bases_to_write) > -1:
45 READ2_MAX_BASES_TO_WRITE="${read2_max_bases_to_write}" 47 READ2_MAX_BASES_TO_WRITE="${read2_max_bases_to_write}"
46 #end if 48 #end if
47 49
48 INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}" 50 INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}"
49
50 51
51 VALIDATION_STRINGENCY="${validation_stringency}" 52 VALIDATION_STRINGENCY="${validation_stringency}"
52 QUIET=true 53 QUIET=true
53 VERBOSITY=ERROR 54 VERBOSITY=ERROR
54 @TMPDIR_OPTION@ 55 @TMPDIR_OPTION@
55 56
56 ]]></command> 57 ]]></command>
57 <inputs> 58 <inputs>
58 59
59 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> 60 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
60 <param name="output_per_rg" type="boolean" checked="False" label="Do you want to output a fastq file per read group (two fastq files per read group if the group is paired)" help="OUTPUT_PER_RG; default=False"/> 61 <param name="single_or_paired" type="select" label="Output format">
62 <option value="se" >Single-end</option>
63 <option value="pe_interleaved" selected="true">Paired-end (one interleaved output file)</option>
64 <option value="pe_sep">Paired-end (two separate output files)</option>
65 </param>
66
61 <param name="re_reverse" type="boolean" checked="True" label="Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq" help="RE_REVERSE; default=True"/> 67 <param name="re_reverse" type="boolean" checked="True" label="Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq" help="RE_REVERSE; default=True"/>
62 <param name="interleave" type="boolean" label="Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe which end it came from" help="INTERLEAVE; default=False"/>
63 <param name="include_non_pf_reads" type="boolean" label="Include non-PF reads from the SAM/BAM dataset into the output FASTQ" help="INCLUDE_NON_PF_READS; PF means 'passes filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads; default=False"/> 68 <param name="include_non_pf_reads" type="boolean" label="Include non-PF reads from the SAM/BAM dataset into the output FASTQ" help="INCLUDE_NON_PF_READS; PF means 'passes filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads; default=False"/>
64 <param name="clipping_attribute" type="text" value="null" label="The attribute that stores the position at which the SAM/BAM record should be clipped" help="CLIPPING_ATTRIBUTE; default=null"/> 69 <param name="clipping_attribute" type="text" value="" label="The attribute that stores the position at which the SAM/BAM record should be clipped" help="CLIPPING_ATTRIBUTE; default=null"/>
65 <param name="clipping_action" type="text" value="null" label="The action that should be taken with clipped reads: 'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region" help="CLIPPING_ACTION; default=null"/> 70 <param name="clipping_action" type="text" value="" label="The action that should be taken with clipped reads: 'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region" help="CLIPPING_ACTION; default=null"/>
66 <param name="read1_trim" type="integer" value="0" min="0" label="The number of bases to trim from the beginning of read 1" help="READ1_TRIM; default=0"/> 71 <param name="read1_trim" type="integer" value="0" min="0" label="The number of bases to trim from the beginning of read 1" help="READ1_TRIM; default=0"/>
67 <param name="read1_max_bases_to_write" type="integer" value="-1" label="The maximum number of bases to write from read 1 after trimming" help="READ1_MAX_BASES_TO_WRITE; If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written; default=null (-1)"/> 72 <param name="read1_max_bases_to_write" type="integer" value="-1" label="The maximum number of bases to write from read 1 after trimming" help="READ1_MAX_BASES_TO_WRITE; If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written; default=null (-1)"/>
68 <param name="read2_trim" type="integer" value="0" min="0" label="The number of bases to trim from the beginning of read 2" help="READ2_TRIM; default=0"/> 73 <param name="read2_trim" type="integer" value="0" min="0" label="The number of bases to trim from the beginning of read 2" help="READ2_TRIM; default=0"/>
69 <param name="read2_max_bases_to_write" type="integer" value="-1" label="The maximum number of bases to write from read 2 after trimming" help="READ2_MAX_BASES_TO_WRITE; If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written; default=null (-1)"/> 74 <param name="read2_max_bases_to_write" type="integer" value="-1" label="The maximum number of bases to write from read 2 after trimming" help="READ2_MAX_BASES_TO_WRITE; If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written; default=null (-1)"/>
70 <param name="include_non_primary_alignments" type="boolean" label="If true, include non-primary alignments in the output" help="INCLUDE_NON_PRIMARY_ALIGNMENTS; Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments; default=False"/> 75 <param name="include_non_primary_alignments" type="boolean" label="If true, include non-primary alignments in the output" help="INCLUDE_NON_PRIMARY_ALIGNMENTS; Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments; default=False"/>
72 <expand macro="VS" /> 77 <expand macro="VS" />
73 78
74 </inputs> 79 </inputs>
75 80
76 <outputs> 81 <outputs>
77 <!-- here dataset discovery is based on fact that if OUTPUT_PER_RG=true this tool automatically adds .fastq extension to emitted files --> 82 <data format="fastqsanger" name="fq_single" label="${tool.name} on ${on_string}: reads as fastq">
78 <data format="txt" name="report" label="SamToFastq run" hidden="true"> 83 <filter>output_type['single_or_paired'] == 'se'</filter>
79 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fastq" ext="fastqsanger" visible="true"/> 84 </data>
85
86 <data format="fastqsanger" name="interleaved_fastq" label="Interleaved pairs from ${tool.name} on ${on_string}">
87 <filter>output_type['single_or_paired'] == 'pe_interleaved'</filter>
88 </data>
89
90 <data format="fastqsanger" name="fq1" label="Paired-end forward strand from ${tool.name} on ${on_string}">
91 <filter>output_type['single_or_paired'] == 'pe_sep'</filter>
92 </data>
93
94 <data format="fastqsanger" name="fq2" label="Paired-end reverse strand from ${tool.name} on ${on_string}">
95 <filter>output_type['single_or_paired'] == 'pe_sep'</filter>
96 </data>
97
98 <data format="fastqsanger" name="fq_u" label="Paired-end unpaired reads from ${tool.name} on ${on_string}">
99 <filter>output_type['single_or_paired'] == 'pe_sep'</filter>
80 </data> 100 </data>
81 </outputs> 101 </outputs>
82 102
83 <tests> 103 <tests>
84 <test> 104 <test>
85 <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/> 105 <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
106 <param name="single_or_paired" value="pe_interleaved" />
86 <param name="output_per_rg" value="false"/> 107 <param name="output_per_rg" value="false"/>
87 <param name="re_reverse" value="true"/> 108 <param name="re_reverse" value="true"/>
88 <param name="interleave" value="true"/>
89 <param name="include_non_pf_reads" value="false"/> 109 <param name="include_non_pf_reads" value="false"/>
90 <param name="clipping_attribute" value="null" /> 110 <param name="clipping_attribute" value="" />
91 <param name="clipping_action" value="null" /> 111 <param name="clipping_action" value="" />
92 <param name="read1_trim" value="0" /> 112 <param name="read1_trim" value="0" />
93 <param name="read1_max_bases_to_write" value="-1"/> 113 <param name="read1_max_bases_to_write" value="-1"/>
94 <param name="read2_trim" value="0" /> 114 <param name="read2_trim" value="0" />
95 <param name="read2_max_bases_to_write" value="-1"/> 115 <param name="read2_max_bases_to_write" value="-1"/>
96 <param name="include_non_primary_alignments" value="false"/> 116 <param name="include_non_primary_alignments" value="false"/>
97 <output name="report"> 117 <output name="interleaved_fastq" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/>
98 <assert_contents> 118 </test>
99 <has_line line="BAM" /> 119 <test>
100 </assert_contents> 120 <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
101 <discovered_dataset designation="INTERLEAVED" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/> 121 <param name="single_or_paired" value="pe_sep" />
102 </output> 122 <param name="output_per_rg" value="false"/>
123 <param name="re_reverse" value="true"/>
124 <param name="include_non_pf_reads" value="false"/>
125 <param name="clipping_attribute" value="" />
126 <param name="clipping_action" value="" />
127 <param name="read1_trim" value="0" />
128 <param name="read1_max_bases_to_write" value="-1"/>
129 <param name="read2_trim" value="0" />
130 <param name="read2_max_bases_to_write" value="-1"/>
131 <param name="include_non_primary_alignments" value="false"/>
132 <output name="fq1" file="picard_SamToFastq_1.fq" ftype="fastqsanger"/>
133 <output name="fq2" file="picard_SamToFastq_2.fq" ftype="fastqsanger"/>
134 <output name="fq_u" file="picard_SamToFastq_u.fq" ftype="fastqsanger"/>
135 </test>
136 <test>
137 <param name="inputFile" value="picard_SamToFastq_se.bam" ftype="bam"/>
138 <param name="single_or_paired" value="se" />
139 <param name="output_per_rg" value="false"/>
140 <param name="re_reverse" value="true"/>
141 <param name="include_non_pf_reads" value="false"/>
142 <param name="clipping_attribute" value="" />
143 <param name="clipping_action" value="" />
144 <param name="read1_trim" value="0" />
145 <param name="read1_max_bases_to_write" value="-1"/>
146 <param name="read2_trim" value="0" />
147 <param name="read2_max_bases_to_write" value="-1"/>
148 <param name="include_non_primary_alignments" value="false"/>
149 <output name="fq_single" file="picard_SamToFastq_se.fq" ftype="fastqsanger"/>
103 </test> 150 </test>
104 </tests> 151 </tests>
105 152
106 153
107 <help> 154 <help>