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comparison picard_SamToFastq.xml @ 27:fdca9493e09b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 70d2a66c405be58d4413753792bcadf212a4da84
author iuc
date Sat, 25 Feb 2023 20:32:54 +0000
parents e65f2d5fd3d8
children c943f4a04af0
comparison
equal deleted inserted replaced
26:fc3866ddc7b6 27:fdca9493e09b
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@">2</token> 5 <token name="@WRAPPER_VERSION@">3</token>
6 </macros> 6 </macros>
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">picard_samtofastq</xref> 8 <xref type="bio.tools">picard_samtofastq</xref>
9 </xrefs> 9 </xrefs>
10 <expand macro="requirements" /> 10 <expand macro="requirements" />
105 105
106 <tests> 106 <tests>
107 <test> 107 <test>
108 <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/> 108 <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
109 <param name="single_or_paired" value="pe_interleaved" /> 109 <param name="single_or_paired" value="pe_interleaved" />
110 <param name="output_per_rg" value="false"/>
111 <param name="re_reverse" value="true"/> 110 <param name="re_reverse" value="true"/>
112 <param name="include_non_pf_reads" value="false"/> 111 <param name="include_non_pf_reads" value="false"/>
113 <param name="clipping_attribute" value="" /> 112 <param name="clipping_attribute" value="" />
114 <param name="clipping_action" value="" /> 113 <param name="clipping_action" value="" />
115 <param name="read1_trim" value="0" /> 114 <param name="read1_trim" value="0" />
120 <output name="interleaved_fastq" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/> 119 <output name="interleaved_fastq" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/>
121 </test> 120 </test>
122 <test> 121 <test>
123 <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/> 122 <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
124 <param name="single_or_paired" value="pe_sep" /> 123 <param name="single_or_paired" value="pe_sep" />
125 <param name="output_per_rg" value="false"/>
126 <param name="re_reverse" value="true"/> 124 <param name="re_reverse" value="true"/>
127 <param name="include_non_pf_reads" value="false"/> 125 <param name="include_non_pf_reads" value="false"/>
128 <param name="clipping_attribute" value="" /> 126 <param name="clipping_attribute" value="" />
129 <param name="clipping_action" value="" /> 127 <param name="clipping_action" value="" />
130 <param name="read1_trim" value="0" /> 128 <param name="read1_trim" value="0" />
137 <output name="fq_u" file="picard_SamToFastq_u.fq" ftype="fastqsanger"/> 135 <output name="fq_u" file="picard_SamToFastq_u.fq" ftype="fastqsanger"/>
138 </test> 136 </test>
139 <test> 137 <test>
140 <param name="inputFile" value="picard_SamToFastq_se.bam" ftype="bam"/> 138 <param name="inputFile" value="picard_SamToFastq_se.bam" ftype="bam"/>
141 <param name="single_or_paired" value="se" /> 139 <param name="single_or_paired" value="se" />
142 <param name="output_per_rg" value="false"/>
143 <param name="re_reverse" value="true"/> 140 <param name="re_reverse" value="true"/>
144 <param name="include_non_pf_reads" value="false"/> 141 <param name="include_non_pf_reads" value="false"/>
145 <param name="clipping_attribute" value="" /> 142 <param name="clipping_attribute" value="" />
146 <param name="clipping_action" value="" /> 143 <param name="clipping_action" value="" />
147 <param name="read1_trim" value="0" /> 144 <param name="read1_trim" value="0" />
162 159
163 ----- 160 -----
164 161
165 .. class:: warningmark 162 .. class:: warningmark
166 163
167 **DANGER: Multiple Outputs**
168
169 Generating per readgroup fastq (setting **OUTPUT_PER_RG** to True) may produce very large numbers of outputs. Know what you are doing!
170
171 @dataset_collections@ 164 @dataset_collections@
172 165
173 @description@ 166 @description@
174 167
175 FASTQ=File 168 FASTQ=File
176 F=File Output fastq file (single-end fastq or, if paired, first end of the pair fastq). 169 F=File Output fastq file (single-end fastq or, if paired, first end of the pair fastq).
177 Required. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG) 170 Required.
178 171
179 SECOND_END_FASTQ=File 172 SECOND_END_FASTQ=File
180 F2=File Output fastq file (if paired, second end of the pair fastq). Default value: null. 173 F2=File Output fastq file (if paired, second end of the pair fastq). Default value: null.
181 Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG) 174
182 175
183 UNPAIRED_FASTQ=File 176 UNPAIRED_FASTQ=File
184 FU=File Output fastq file for unpaired reads; may only be provided in paired-fastq mode Default 177 FU=File Output fastq file for unpaired reads; may only be provided in paired-fastq mode Default
185 value: null. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG) 178 value: null.
186
187 OUTPUT_PER_RG=Boolean
188 OPRG=Boolean Output a fastq file per read group (two fastq files per read group if the group is
189 paired). Default value: false. Possible values: {true, false} Cannot be used in
190 conjuction with option(s) SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F)
191
192 OUTPUT_DIR=File
193 ODIR=File Directory in which to output the fastq file(s). Used only when OUTPUT_PER_RG is true.
194 Default value: null.
195 179
196 RE_REVERSE=Boolean 180 RE_REVERSE=Boolean
197 RC=Boolean Re-reverse bases and qualities of reads with negative strand flag set before writing them 181 RC=Boolean Re-reverse bases and qualities of reads with negative strand flag set before writing them
198 to fastq Default value: true. Possible values: {true, false} 182 to fastq Default value: true. Possible values: {true, false}
199 183