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comparison fasterq_dump.xml @ 19:248f85ff0733 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 1e2492fa4557ddc6ffefc16b249ed9ef0207d5e1"
author iuc
date Tue, 23 Jun 2020 17:18:45 -0400
parents 7068f48d0ef9
children 964579f93c54
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18:7068f48d0ef9 19:248f85ff0733
1 <tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy0" profile="18.01"> 1 <tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy1" profile="18.01">
2 <description>format from NCBI SRA</description> 2 <description>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"/>
167 </output_collection> 167 </output_collection>
168 <output_collection name="output_collection" type="list"> 168 <output_collection name="output_collection" type="list">
169 <element name="SRR002702" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> 169 <element name="SRR002702" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
170 </output_collection> 170 </output_collection>
171 </test> 171 </test>
172 <test>
173 <param name="input_select" value="file_list"/>
174 <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
175 <output_collection name="list_paired" type="list:paired">
176 <element name="SRR11857975">
177 <element name="forward" file="SRR11857975_1.fastq.gz" decompress="True">
178 </element>
179 <element name="reverse" file="SRR11857975_2.fastq.gz" decompress="True">
180 </element>
181 </element>
182 </output_collection>
183 </test>
184 <test>
185 <param name="input_select" value="file_list"/>
186 <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
187 <output_collection name="list_paired" type="list:paired">
188 <element name="SRR11953971">
189 <element name="forward" file="SRR11953971_1.fastq.gz" decompress="True"/>
190 <element name="reverse" file="SRR11953971_2.fastq.gz" decompress="True"/>
191 </element>
192 </output_collection>
193 </test>
172 </tests> 194 </tests>
173 <help><![CDATA[ 195 <help><![CDATA[
174 **What it does?** 196 **What it does?**
175 197
176 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. 198 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.