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comparison fasterq_dump.xml @ 26:f7732611d0fc draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 7632986831e24fcd189a57d824b9e6b1d5dc5c4c
author iuc
date Mon, 26 Aug 2024 14:59:07 +0000
parents 6669afa92957
children
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25:0c5a5e670ac0 26:f7732611d0fc
11 set -o | grep -q pipefail && set -o pipefail; 11 set -o | grep -q pipefail && set -o pipefail;
12 @COPY_CONFIGFILE@ 12 @COPY_CONFIGFILE@
13 @CONFIGURE_RETRY@ 13 @CONFIGURE_RETRY@
14 @SET_ACCESSIONS@ 14 @SET_ACCESSIONS@
15 while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do 15 while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
16 fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1} 16 fasterq-dump "\$acc"
17 --seq-defline '@\$sn/\$ri' 17 -e \${GALAXY_SLOTS:-1}
18 -t \${TMPDIR}
19 --seq-defline '$adv.seq_defline'
18 --qual-defline '+' 20 --qual-defline '+'
19 $adv.split 21 $adv.split
20 #if str( $adv.minlen ) != "": 22 #if str( $adv.minlen ) != "":
21 --min-read-len "$adv.minlen" 23 --min-read-len "$adv.minlen"
22 #end if 24 #end if
69 </command> 71 </command>
70 <expand macro="configfile_hack"/> 72 <expand macro="configfile_hack"/>
71 <inputs> 73 <inputs>
72 <expand macro="input_conditional"/> 74 <expand macro="input_conditional"/>
73 <section name="adv" title="Advanced Options" expanded="False"> 75 <section name="adv" title="Advanced Options" expanded="False">
76 <expand macro="defline" defline_param="--seq-defline" defline_default="@$ac.$sn/$ri"/>
74 <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--min-read-len"/> 77 <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--min-read-len"/>
75 <param name="split" type="select" display="radio" label="Select how to split the spots" help="This option will only be used when there are multiple reads per spot (for example paired-end)."> 78 <param name="split" type="select" display="radio" label="Select how to split the spots" help="This option will only be used when there are multiple reads per spot (for example paired-end).">
76 <option value="--split-3">--split-3: write properly paired biological reads into different files and single reads in another file</option> 79 <option value="--split-3">--split-3: write properly paired biological reads into different files and single reads in another file</option>
77 <option value="--split-files">--split-files: write reads into different files (forward and reverse may not match if one read is empty)</option> 80 <option value="--split-files">--split-files: write reads into different files (forward and reverse may not match if one read is empty)</option>
78 <option value="--split-spot">--split-spot: split spots into reads (only one output file)</option> 81 <option value="--split-spot">--split-spot: split spots into reads (only one output file)</option>
184 <element name="forward" file="SRR11953971_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> 187 <element name="forward" file="SRR11953971_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
185 <element name="reverse" file="SRR11953971_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> 188 <element name="reverse" file="SRR11953971_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
186 </element> 189 </element>
187 </output_collection> 190 </output_collection>
188 </test> 191 </test>
192 <test expect_num_outputs="4">
193 <param name="input_select" value="file_list"/>
194 <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
195 <section name="adv">
196 <param name="seq_defline" value="@$ac.$si/$ri $sn length=$rl"/>
197 </section>
198 <output_collection name="list_paired" type="list:paired" count="1">
199 <element name="SRR11953971">
200 <element name="forward" ftype="fastqsanger.gz" decompress="True">
201 <assert_contents>
202 <!-- TODO replace has_size by has_line -->
203 <has_size min="56206"/>
204 <!-- <has_line line="@SRR11953971.2053/1 2053 length=101"/> -->
205 </assert_contents>
206 </element>
207 <element name="reverse" ftype="fastqsanger.gz" decompress="True">
208 <assert_contents>
209 <has_size min="59843"/>
210 <!-- <has_line line="@SRR11953971.2053/2 2053 length=101"/> -->
211 </assert_contents>
212 </element>
213 </element>
214 </output_collection>
215 </test>
189 </tests> 216 </tests>
190 <help><![CDATA[ 217 <help><![CDATA[
191 **What it does?** 218 **What it does?**
192 219
193 This tool extracts data (in fastq_ format) from the Short Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). It is based on the fasterq-dump_ utility of the SRA Toolkit. The following applies: 220 This tool extracts data (in fastq_ format) from the Short Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). It is based on the fasterq-dump_ utility of the SRA Toolkit. The following applies: