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comparison fastq_dump.xml @ 15:54366e4d692a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
author iuc
date Fri, 20 Mar 2020 16:36:52 +0000
parents 74dd3d0a33d1
children 37f09413ddbf
comparison
equal deleted inserted replaced
14:5c5d6624f8de 15:54366e4d692a
1 <tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@.3"> 1 <tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" 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"/>
7 <version_command>fastq-dump --version</version_command> 7 <version_command>fastq-dump --version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9
10 @SET_ACCESSIONS@ 9 @SET_ACCESSIONS@
11 10
12 ## Need to set the home directory to the current working directory, 11 ## Need to set the home directory to the current working directory,
13 ## else the tool tries to write to home/.ncbi and fails when used 12 ## else the tool tries to write to home/.ncbi and fails when used
14 ## with a cluster manager. 13 ## with a cluster manager.
15 export HOME=\$PWD && 14 @CONFIGURE_TIMEOUT@
16 vdb-config --restore-defaults &&
17 #if $input.input_select == "file": 15 #if $input.input_select == "file":
18 fastq-dump --log-level fatal --accession '${input.file.name}' 16 fastq-dump --log-level fatal --accession '${input.file.name}'
19 #else: 17 #else:
20 vdb-config -s "/repository/user/main/public/root=\$PWD" && 18 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
21 ## Do not use prefetch if region is specified, to avoid downloading 19 ## Do not use prefetch if region is specified, to avoid downloading
22 ## the complete sra file. 20 ## the complete sra file.
23 #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ): 21 #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ):
24 ASCP_PATH=`command -v ascp` && 22 prefetch -X 200000000 "\$acc" &&
25 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
26 prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
27 ## Duplicate vdb-config, in case settings changed between prefetch and 23 ## Duplicate vdb-config, in case settings changed between prefetch and
28 ## dump command. 24 ## dump command.
29 vdb-config -s "/repository/user/main/public/root=\$PWD" && 25 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
30 #end if 26 #end if
31 fastq-dump --accession "\$acc" 27 fastq-dump --accession "\$acc"
68 #if str( $outputformat ) == "fastqsanger.gz": 64 #if str( $outputformat ) == "fastqsanger.gz":
69 --gzip 65 --gzip
70 #elif str( $outputformat ) == "fastqsanger.bz2": 66 #elif str( $outputformat ) == "fastqsanger.bz2":
71 --bzip2 67 --bzip2
72 #end if 68 #end if
69
70 #if str($adv.table) != "":
71 --table $adv.table
72 #end if
73
74
73 #if $input.input_select=="file": 75 #if $input.input_select=="file":
74 --stdout 76 --stdout
75 "$input.file" > "$output_file" 77 "$input.file" > "$output_file"
76 78
77 #elif $input.input_select=="accession_number": 79 #elif $input.input_select=="accession_number":
78 --stdout 80 --stdout
79 "\$acc" > "$output_accession" ) 81 "\$acc" > "$output_accession" )
80 #end if 82 #end if
81 83
82 #if $input.input_select=="file_list": 84 #if $input.input_select=="file_list":
85 "\$acc"
83 ) ; done 86 ) ; done
84 87
85 ; 88 ;
86 89
87 for i in `ls *.fast* | cut -f 1 -d '_' | uniq` ; do 90 for i in `ls *.fast* | cut -f 1 -d '_' | uniq` ; do
124 <option value="redacted">redacted</option> 127 <option value="redacted">redacted</option>
125 </param> 128 </param>
126 <param name="spotgroups" type="text" label="Filter by spot-groups" optional="true" argument="--spot-groups"/> 129 <param name="spotgroups" type="text" label="Filter by spot-groups" optional="true" argument="--spot-groups"/>
127 <param name="clip" type="boolean" truevalue="--clip" falsevalue="" argument="--clip" label="Apply left and right clips" /> 130 <param name="clip" type="boolean" truevalue="--clip" falsevalue="" argument="--clip" label="Apply left and right clips" />
128 <param name="skip_technical" type="boolean" truevalue="--skip-technical" falsevalue="" checked="False" label="Dump only biological reads" argument="--skip-technical"/> 131 <param name="skip_technical" type="boolean" truevalue="--skip-technical" falsevalue="" checked="False" label="Dump only biological reads" argument="--skip-technical"/>
132 <param name="table" label="Table name within cSRA object" type="text" value="" optional="true" help="For SRA of noisy long-reads put SEQUENCE" argument="--table"/>
129 </section> 133 </section>
130 </inputs> 134 </inputs>
131 <outputs> 135 <outputs>
132 <collection name="list_paired" type="list:paired" label="Pair-end data (fastq-dump)"> 136 <collection name="list_paired" type="list:paired" label="Pair-end data (fastq-dump)">
133 <filter>input['input_select'] == "file_list"</filter> 137 <filter>input['input_select'] == "file_list"</filter>
224 <param name="file_list" value="list_se"/> 228 <param name="file_list" value="list_se"/>
225 <param name="maxID" value="5"/> 229 <param name="maxID" value="5"/>
226 <output_collection name="output_collection" type="list"> 230 <output_collection name="output_collection" type="list">
227 <element name="SRR1993644" file="SRR1993644.fastqsanger"/> 231 <element name="SRR1993644" file="SRR1993644.fastqsanger"/>
228 </output_collection> 232 </output_collection>
229 </test> 233 </test>
234 <test>
235 <param name="input_select" value="accession_number"/>
236 <param name="outputformat" value="fastqsanger.gz"/>
237 <param name="accession" value="SRR6982805"/>
238 <param name="maxID" value="2"/>
239 <param name="table" value="SEQUENCE"/>
240 <output name="output_accession" file="SRR6982805.fastqsanger.gz" ftype="fastqsanger.gz" decompress="True"/>
241 </test>
230 </tests> 242 </tests>
231 <help><![CDATA[ 243 <help><![CDATA[
232 **What it does?** 244 **What it does?**
233 245
234 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 fastq-dump_ utility of the SRA Toolkit. 246 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 fastq-dump_ utility of the SRA Toolkit.