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comparison picard_SamToFastq.xml @ 32:f9242e01365a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309
author iuc
date Mon, 25 Sep 2023 08:32:17 +0000
parents 585027e65f3b
children 3f254c5ced1d
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31:585027e65f3b 32:f9242e01365a
53 INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}" 53 INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}"
54 54
55 VALIDATION_STRINGENCY="${validation_stringency}" 55 VALIDATION_STRINGENCY="${validation_stringency}"
56 QUIET=true 56 QUIET=true
57 VERBOSITY=ERROR 57 VERBOSITY=ERROR
58 @TMPDIR_OPTION@
59 58
60 ]]></command> 59 ]]></command>
61 <inputs> 60 <inputs>
62 61
63 <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"/> 62 <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"/>
102 <filter>output_type['single_or_paired'] == 'pe_sep'</filter> 101 <filter>output_type['single_or_paired'] == 'pe_sep'</filter>
103 </data> 102 </data>
104 </outputs> 103 </outputs>
105 104
106 <tests> 105 <tests>
107 <test> 106 <test expect_num_outputs="5">
108 <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/> 107 <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
109 <param name="single_or_paired" value="pe_interleaved" /> 108 <param name="single_or_paired" value="pe_interleaved" />
110 <param name="re_reverse" value="true"/> 109 <param name="re_reverse" value="true"/>
111 <param name="include_non_pf_reads" value="false"/> 110 <param name="include_non_pf_reads" value="false"/>
112 <param name="clipping_attribute" value="" /> 111 <param name="clipping_attribute" value="" />
116 <param name="read2_trim" value="0" /> 115 <param name="read2_trim" value="0" />
117 <param name="read2_max_bases_to_write" value="-1"/> 116 <param name="read2_max_bases_to_write" value="-1"/>
118 <param name="include_non_primary_alignments" value="false"/> 117 <param name="include_non_primary_alignments" value="false"/>
119 <output name="interleaved_fastq" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/> 118 <output name="interleaved_fastq" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/>
120 </test> 119 </test>
121 <test> 120 <test expect_num_outputs="5">
122 <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/> 121 <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
123 <param name="single_or_paired" value="pe_sep" /> 122 <param name="single_or_paired" value="pe_sep" />
124 <param name="re_reverse" value="true"/> 123 <param name="re_reverse" value="true"/>
125 <param name="include_non_pf_reads" value="false"/> 124 <param name="include_non_pf_reads" value="false"/>
126 <param name="clipping_attribute" value="" /> 125 <param name="clipping_attribute" value="" />
132 <param name="include_non_primary_alignments" value="false"/> 131 <param name="include_non_primary_alignments" value="false"/>
133 <output name="fq1" file="picard_SamToFastq_1.fq" ftype="fastqsanger"/> 132 <output name="fq1" file="picard_SamToFastq_1.fq" ftype="fastqsanger"/>
134 <output name="fq2" file="picard_SamToFastq_2.fq" ftype="fastqsanger"/> 133 <output name="fq2" file="picard_SamToFastq_2.fq" ftype="fastqsanger"/>
135 <output name="fq_u" file="picard_SamToFastq_u.fq" ftype="fastqsanger"/> 134 <output name="fq_u" file="picard_SamToFastq_u.fq" ftype="fastqsanger"/>
136 </test> 135 </test>
137 <test> 136 <test expect_num_outputs="5">
138 <param name="inputFile" value="picard_SamToFastq_se.bam" ftype="bam"/> 137 <param name="inputFile" value="picard_SamToFastq_se.bam" ftype="bam"/>
139 <param name="single_or_paired" value="se" /> 138 <param name="single_or_paired" value="se" />
140 <param name="re_reverse" value="true"/> 139 <param name="re_reverse" value="true"/>
141 <param name="include_non_pf_reads" value="false"/> 140 <param name="include_non_pf_reads" value="false"/>
142 <param name="clipping_attribute" value="" /> 141 <param name="clipping_attribute" value="" />
155 154
156 **Purpose** 155 **Purpose**
157 156
158 Extracts read sequences and qualities from the input SAM/BAM dataset and outputs them in Sanger fastq format. In the RE_REVERSE=True mode (default behavior), if the read is aligned and the alignment is to the reverse strand on the genome, the read's sequence from input SAM.BAM dataset will be reverse-complemented prior to writing it to fastq in order restore correctly the original read sequence as it was generated by the sequencer. 157 Extracts read sequences and qualities from the input SAM/BAM dataset and outputs them in Sanger fastq format. In the RE_REVERSE=True mode (default behavior), if the read is aligned and the alignment is to the reverse strand on the genome, the read's sequence from input SAM.BAM dataset will be reverse-complemented prior to writing it to fastq in order restore correctly the original read sequence as it was generated by the sequencer.
159 158
160 -----
161
162 .. class:: warningmark 159 .. class:: warningmark
160
163 161
164 @dataset_collections@ 162 @dataset_collections@
165 163
166 @description@ 164 @description@
167 165