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comparison fastq_dump.xml @ 6:892dcc4ceff2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit ee50324111351323cc294e051a6fab1733a89ec1
author iuc
date Wed, 22 Mar 2017 05:23:18 -0400
parents de3b6a854c0a
children 52a8ae1be0d5
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5:7a8fa6facf55 6:892dcc4ceff2
1 <tool id="fastq_dump" name="Extract reads" version="@VERSION@"> 1 <tool id="fastq_dump" name="Extract reads" version="@VERSION@.1">
2 <description>in FASTQ/A format from NCBI SRA.</description> 2 <description>in FASTQ/A format from NCBI SRA.</description>
3 <macros> 3 <macros>
4 <import>sra_macros.xml</import> 4 <import>sra_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
91 ) ; done 91 ) ; done
92 92
93 ; 93 ;
94 94
95 95
96 #if str( $outputformat ) == "fasta": 96
97 97
98 for f in *_2.fasta ; do mv "\$f" "`basename \$f _2.fasta`_reverse.fasta" ; mv "`basename \$f _2.fasta`_1.fasta" "`basename \$f _2.fasta`_forward.fasta" ; done && 98
99 for f in *_1.fasta; do mv "\$f" "`basename \$f _1.fasta`__single.fasta"; done 99 for i in `ls *.fast* | cut -f 1 -d '_' | uniq` ; do
100 100 count=`ls \$i* | wc -l` ;
101 #else: 101 data=(\$(ls -d \$i*));
102 102
103 for f in *_2.fastq ; do mv "\$f" "`basename \$f _2.fastq`_reverse.fastq" ; mv "`basename \$f _2.fastq`_1.fastq" "`basename \$f _2.fastq`_forward.fastq" ; done && 103 if [ "\$count" -eq 2 ]; then
104 for f in *_1.fastq; do mv "\$f" "`basename \$f _1.fastq`__single.fastq"; done 104 mv "\${data[0]}" "\${data[0]}"_forward.$outputformat; mv "\${data[1]}" "\${data[1]}"_reverse.$outputformat ;
105 105 elif [ "\$count" -eq 1 ]; then
106 #end if 106 mv "\${data[0]}" "\${data[0]}"__single.$outputformat ;
107 107 fi;
108 108 done
109
110 109
111 110
112 #end if 111 #end if
113 112
114 113
151 <!-- Use named regex group to grab pattern 150 <!-- Use named regex group to grab pattern
152 <identifier_0>_<identifier_1>.fq. Here identifier_0 is the list 151 <identifier_0>_<identifier_1>.fq. Here identifier_0 is the list
153 identifier in the nested collection and identifier_1 is either 152 identifier in the nested collection and identifier_1 is either
154 forward or reverse (for instance samp1_forward.fq). 153 forward or reverse (for instance samp1_forward.fq).
155 --> 154 -->
156 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastq" ext="fastqsanger" visible="false" /> 155 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_\d+.fastq_(?P&lt;identifier_1&gt;[^_]+)\.fastq" ext="fastqsanger" visible="false" />
157 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fasta" ext="fasta" visible="false" /> 156 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_\d+.fasta_(?P&lt;identifier_1&gt;[^_]+)\.fasta" ext="fasta" visible="false" />
158 </collection> 157 </collection>
159 <collection name="output_collection" type='list' label="Single-end Fast(q|a)"> 158 <collection name="output_collection" type='list' label="Single-end Fast(q|a)">
160 <filter>input['input_select'] == "file_list"</filter> 159 <filter>input['input_select'] == "file_list"</filter>
161 <discover_datasets pattern="(?P&lt;designation&gt;.+)__single\.fastq" directory="." ext='fastqsanger'/> 160 <discover_datasets pattern="(?P&lt;designation&gt;.+)_\d+.fastq__single\.fastq" directory="." ext='fastqsanger'/>
162 <discover_datasets pattern="(?P&lt;designation&gt;.+)__single\.fasta" directory="." ext='fasta'/> 161 <discover_datasets pattern="(?P&lt;designation&gt;.+)_\d+.fasta__single\.fasta" directory="." ext='fasta'/>
163 </collection> 162 </collection>
164 <data format="fastqsanger" name="output_accession" > 163 <data format="fastqsanger" name="output_accession" >
165 <filter>input['input_select'] == "accession_number"</filter> 164 <filter>input['input_select'] == "accession_number"</filter>
166 <change_format> 165 <change_format>
167 <when input="outputformat" value="fasta" format="fasta"/> 166 <when input="outputformat" value="fasta" format="fasta"/>
192 <param name="outputformat" value="fastqsanger"/> 191 <param name="outputformat" value="fastqsanger"/>
193 <param name="accession" value="SRR925743"/> 192 <param name="accession" value="SRR925743"/>
194 <param name="maxID" value="5"/> 193 <param name="maxID" value="5"/>
195 <output name="output_accession" file="fastq_dump_result.fastq" ftype="fastqsanger"/> 194 <output name="output_accession" file="fastq_dump_result.fastq" ftype="fastqsanger"/>
196 </test> 195 </test>
196 <test>
197 <param name="input_select" value="file_list"/>
198 <param name="outputformat" value="fastqsanger"/>
199 <param name="file_list" value="list_pe"/>
200 <param name="maxID" value="5"/>
201 <output_collection name="list_paired" type="list:paired">
202 <element name="DRR015708">
203 <element name="forward" file="DRR015708_forward.fastqsanger">
204 </element>
205 <element name="reverse" file="DRR015708_reverse.fastqsanger">
206 </element>
207 </element>
208 </output_collection>
209 </test>
210 <test>
211 <param name="input_select" value="file_list"/>
212 <param name="outputformat" value="fastqsanger"/>
213 <param name="file_list" value="list_pe2"/>
214 <param name="maxID" value="5"/>
215 <output_collection name="list_paired" type="list:paired">
216 <element name="ERR027433">
217 <element name="forward" file="ERR027433_forward.fastqsanger">
218 </element>
219 <element name="reverse" file="ERR027433_reverse.fastqsanger">
220 </element>
221 </element>
222 </output_collection>
223 </test>
224 <test>
225 <param name="input_select" value="file_list"/>
226 <param name="outputformat" value="fastqsanger"/>
227 <param name="file_list" value="list_se"/>
228 <param name="maxID" value="5"/>
229 <output_collection name="output_collection" type="list">
230 <element name="SRR1993644" file="SRR1993644.fastqsanger"/>
231 </output_collection>
232 </test>
197 </tests> 233 </tests>
198 <help> 234 <help>
199 This tool extracts reads from SRA archives using fastq-dump. 235 This tool extracts reads from SRA archives using fastq-dump.
200 The fastq-dump program is developed at NCBI, and is available at 236 The fastq-dump program is developed at NCBI, and is available at
201 http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. 237 http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.