Mercurial > repos > devteam > picard
comparison picard_SamToFastq.xml @ 21:1181366ba593 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit cbe534af56ee782e8d1aa0fa872059d2a5e42db8"
author | iuc |
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date | Mon, 17 Feb 2020 15:23:48 +0000 |
parents | a5a13ea16d17 |
children | 4740a2548206 |
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20:c1aaa5a116d0 | 21:1181366ba593 |
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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<designation>.+)\.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> |