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comparison fastq_dump.xml @ 40:8848455c0270 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 14:59:28 +0000
parents fb723c531be5
children
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39:516a54ddf218 40:8848455c0270
89 <option value="fastqsanger.gz">gzip compressed fastq</option> 89 <option value="fastqsanger.gz">gzip compressed fastq</option>
90 <option value="fastqsanger">Uncompressed fastq</option> 90 <option value="fastqsanger">Uncompressed fastq</option>
91 <option value="fastqsanger.bz2">bzip2 compressed fastq</option> 91 <option value="fastqsanger.bz2">bzip2 compressed fastq</option>
92 </param> 92 </param>
93 <section name="adv" title="Advanced Options" expanded="False"> 93 <section name="adv" title="Advanced Options" expanded="False">
94 <expand macro="defline" defline_param="--defline-seq" defline_default="@$sn[_$rn]/$ri"/> 94 <expand macro="defline" defline_param="--defline-seq" defline_default="@$ac.$sn[_$rn]/$ri"/>
95 <param name="minID" type="integer" label="Minimum spot ID" optional="true" help="Minimum spot id to be dumped." argument="--minSpotId"/> 95 <param name="minID" type="integer" label="Minimum spot ID" optional="true" help="Minimum spot id to be dumped." argument="--minSpotId"/>
96 <param name="maxID" type="integer" label="Maximum spot ID" optional="true" help="Maximum spot id to be dumped." argument="--maxSpotId"/> 96 <param name="maxID" type="integer" label="Maximum spot ID" optional="true" help="Maximum spot id to be dumped." argument="--maxSpotId"/>
97 <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--minReadLen"/> 97 <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--minReadLen"/>
98 <param name="split" type="boolean" checked="true" truevalue="--split-spot" falsevalue="" label="Split spot by read pairs" help="Split spots into individual reads." argument="--split-spot"/> 98 <param name="split" type="boolean" checked="true" truevalue="--split-spot" falsevalue="" label="Split spot by read pairs" help="Split spots into individual reads." argument="--split-spot"/>
99 <expand macro="alignments"/> 99 <expand macro="alignments"/>
277 <section name="adv"> 277 <section name="adv">
278 <param name="defline_seq" value="@$sn/$ri"/> 278 <param name="defline_seq" value="@$sn/$ri"/>
279 </section> 279 </section>
280 <output_collection name="list_paired" type="list:paired" count="1"> 280 <output_collection name="list_paired" type="list:paired" count="1">
281 <element name="SRR522874.sra"> 281 <element name="SRR522874.sra">
282 <element name="forward" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> 282 <element name="forward" file="SRR522874.sra_2_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
283 <element name="reverse" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> 283 <element name="reverse" file="SRR522874.sra_4_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
284 </element> 284 </element>
285 </output_collection> 285 </output_collection>
286 </test> 286 </test>
287 </tests> 287 </tests>
288 <help><![CDATA[ 288 <help><![CDATA[