Mercurial > repos > iuc > sra_tools

annotate fasterq_dump.xml @ 16:aad3885b3216 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
author iuc
date Fri, 20 Mar 2020 12:47:18 -0400
parents f5ea3ce9b9b0
children c441583adae5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
16
aad3885b3216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents: 15
diff changeset
1 <tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy1" profile="18.01">
15
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
2 <description>format from NCBI SRA</description>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
3 <macros>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
4 <import>sra_macros.xml</import>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
5 </macros>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
7 <version_command>fasterq-dump --version</version_command>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
9 @SET_ACCESSIONS@
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
10 #if $input.input_select == "file":
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
11 acc='${input.file.name}' &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
12 ln -s '${input.file}' "\$acc" &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
13 #end if
16
aad3885b3216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents: 15
diff changeset
14 @CONFIGURE_TIMEOUT@
15
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
15 fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
16 $adv.split
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
17 #if str( $adv.minlen ) != "":
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
18 --min-read-len "$adv.minlen"
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
19 #end if
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
20 $adv.skip_technical >> $log 2>&1
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
21 &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
22 mkdir -p output &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
23 mkdir -p outputOther &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
24 count=`ls *.fastq | wc -l` &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
25 echo "There are \$count fastq" &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
26 data=(\$(ls *.fastq)) &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
27 if [ "\$count" -eq 1 ]; then
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
28 gzip -c "\${data[0]}" > output/"\${acc}"__single.fastqsanger.gz &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
29 rm "\${data[0]}";
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
30 elif [ "$adv.split" = "--split-3" ]; then
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
31 if [ -e "\${acc}".fastq ]; then
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
32 gzip -c "\${acc}".fastq > outputOther/"\${acc}"__single.fastqsanger.gz;
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
33 fi &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
34 gzip -c "\${acc}"_1.fastq > output/"\${acc}"_forward.fastqsanger.gz &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
35 gzip -c "\${acc}"_2.fastq > output/"\${acc}"_reverse.fastqsanger.gz &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
36 rm "\${acc}"*.fastq;
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
37 elif [ "\$count" -eq 2 ]; then
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
38 #if $adv.skip_technical:
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
39 gzip -c "\${data[0]}" > output/"\${acc}"_forward.fastqsanger.gz &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
40 gzip -c "\${data[1]}" > output/"\${acc}"_reverse.fastqsanger.gz &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
41 #else
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
42 gzip -c "\${data[0]}" > outputOther/"\${data[0]}"sanger.gz &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
43 gzip -c "\${data[1]}" > outputOther/"\${data[1]}"sanger.gz &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
44 #end if
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
45 rm "\${data[0]}" &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
46 rm "\${data[1]}";
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
47 else
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
48 for file in \${data[*]}; do
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
49 gzip -c "\$file" > outputOther/"\$file"sanger.gz &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
50 rm "\$file";
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
51 done;
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
52 fi;
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
53 #if $input.input_select=="file_list":
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
54 ) ; done
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
55
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
56 ;
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
57 #elif $input.input_select=="accession_number":
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
58 );
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
59 #end if
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
60 ]]>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
61 </command>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
62 <inputs>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
63 <expand macro="input_conditional"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
64 <section name="adv" title="Advanced Options" expanded="False">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
65 <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"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
66 <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).">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
67 <option value="--split-3">--split-3: write properly paired biological reads into different files and single reads in another file</option>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
68 <option value="--split-files">--split-files: write reads into different files (forward and reverse may not match if one read is empty)</option>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
69 <option value="--split-spot">--split-spot: split spots into reads (only one output file)</option>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
70 <option value="--concatenate-reads">--concatenate-reads: writes whole spots into one file</option>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
71 </param>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
72 <param name="skip_technical" type="boolean" truevalue="--skip-technical" falsevalue="--include-technical" checked="True" label="Dump only biological reads" help="Will not be used if --split-3 is selected." argument="--skip-technical/--include-technical"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
73 </section>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
74 </inputs>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
75 <outputs>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
76 <data name="log" format="txt" label="fasterq-dump log"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
77 <collection name="list_paired" type="list:paired" label="Pair-end data (fasterq-dump)">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
78
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
79 <!-- Use named regex group to grab pattern
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
80 <identifier_0>_<identifier_1>.fq. Here identifier_0 is the list
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
81 identifier in the nested collection and identifier_1 is either
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
82 forward or reverse (for instance samp1_forward.fq).
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
83 -->
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
84
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
85 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastqsanger.gz" directory="output" ext="fastqsanger.gz" />
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
86 </collection>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
87 <collection name="output_collection" type='list' label="Single-end data (fasterq-dump)">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
88 <discover_datasets pattern="(?P&lt;designation&gt;.+)__single\.fastqsanger.gz" directory="output" ext='fastqsanger.gz'/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
89 </collection>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
90 <collection name="output_collection_other" type='list' label="Other data (fasterq-dump)">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
91 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fastqsanger\.gz" directory="outputOther" format="fastqsanger.gz"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
92 </collection>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
93 </outputs>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
94 <tests>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
95 <test>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
96 <param name="input_select" value="accession_number"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
97 <param name="accession" value="ERR086330"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
98 <output_collection name="list_paired" type="list:paired">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
99 <element name="ERR086330">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
100 <element name="forward" file="ERR086330_1.fastq.gz" decompress="True">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
101 </element>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
102 <element name="reverse" file="ERR086330_2.fastq.gz" decompress="True">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
103 </element>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
104 </element>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
105 </output_collection>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
106 </test>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
107 <test>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
108 <param name="input_select" value="accession_number"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
109 <param name="accession" value="SRR002702"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
110 <param name="split" value="--split-files"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
111 <param name="skip_technical" value="False"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
112 <output_collection name="output_collection_other" type="list">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
113 <element name="SRR002702_1" file="SRR002702_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
114 <element name="SRR002702_2" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
115 </output_collection>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
116 </test>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
117 <test>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
118 <param name="input_select" value="file"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
119 <param name="file" value="SRR522874.sra"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
120 <param name="split" value="--split-files"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
121 <param name="skip_technical" value="True"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
122 <output_collection name="list_paired" type="list:paired">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
123 <element name="SRR522874.sra">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
124 <element name="forward" file="SRR522874.sra_2.fastq.gz" decompress="True">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
125 </element>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
126 <element name="reverse" file="SRR522874.sra_4.fastq.gz" decompress="True">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
127 </element>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
128 </element>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
129 </output_collection>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
130 </test>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
131 <test>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
132 <param name="input_select" value="file"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
133 <param name="file" value="SRR522874.sra"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
134 <param name="split" value="--split-files"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
135 <param name="skip_technical" value="False"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
136 <output_collection name="output_collection_other" type="list">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
137 <element name="SRR522874.sra_1" file="SRR522874.sra_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
138 <element name="SRR522874.sra_2" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
139 <element name="SRR522874.sra_3" file="SRR522874.sra_3.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
140 <element name="SRR522874.sra_4" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
141 </output_collection>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
142 </test>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
143 <test>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
144 <param name="input_select" value="file_list"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
145 <param name="file_list" value="list_sra"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
146 <param name="minlen" value="21"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
147 <output_collection name="output_collection_other" type="list">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
148 <element name="SRR522874__single" file="SRR522874.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
149 </output_collection>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
150 <output_collection name="list_paired" type="list:paired">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
151 <element name="SRR522874">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
152 <element name="forward" file="SRR522874_1.fastq.gz" decompress="True">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
153 </element>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
154 <element name="reverse" file="SRR522874_2.fastq.gz" decompress="True">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
155 </element>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
156 </element>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
157 </output_collection>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
158 <output_collection name="output_collection" type="list">
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
159 <element name="SRR002702" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
160 </output_collection>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
161 </test>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
162 </tests>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
163 <help><![CDATA[
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
164 **What it does?**
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
165
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
166 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.
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
167
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
168 **How to use it?**
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
169
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
170 There are three ways in which you can download data:
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
171
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
172 1. Data for single accession
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
173 2. Multiple datasets using a list of accessions
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
174 3. Extract data from already uploaded SRA dataset
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
175
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
176 Below we discuss each in detail.
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
177
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
178 ------
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
179
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
180 **Uploading data for a single accession**
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
181
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
182 When you type a single accession number (e.g., `SRR1582967`) into **Accession** box and click **Execute** the tool will fetch data for you.
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
183
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
184 -----
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
185
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
186 **Uploading multiple datasets using a list of accessions**
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
187
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
188 A more realistic scenario is when you want to upload a number of datasets at once. To do this you need a list of accession, where there is only one accession per line (see below for information on how to generate such a file). Once you have this file:
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
189
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
190 1. Upload it into your history using Galaxy's upload tool
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
191 2. Once the list of accessions is uploaded choose *List of SRA accessions, one per line* from **select input type** dropdown
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
192 3. Choose uploaded file within the **sra accession list** field
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
193 4. Click **Execute**
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
194
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
195 -----
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
196
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
197 **Extract data from already uploaded SRA dataset**
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
198
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
199 If a SRA dataset is present in the history, it can be converted into fastq dataset by setting **select input type** drop-down to *SRA archive in current history*. Just like in the case of extracting data for single accession number the following applies:
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
200
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
201 - if data is paired-ended (or mate-pair) the tool will generate a single *interleaved* dataset, in which forward and reverse mates are alternating (see example below).
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
202 - if data is single ended, a standard fastq dataset will be produced
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
203
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
204 -----
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
205
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
206 **Output**
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
207
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
208 In every case, fastq datasets produced will be saved in Galaxy's history as a collection_ - a single history element containing multiple datasets.
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
209 In fact, three collections will be produced: one containing paired-end data, another containing single-end data, and a third one which contains reads which could not be classified.
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
210 Some collections may be empty if the accessions provided in the list does not contain one of the type of data.
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
211
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
212 .. class:: warningmark
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
213
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
214 When you decide to dump technical reads (in Advanced Options Dump only biological reads is set to No), you will probably find your PAIRED data in the other data collection as it is impossible to determine if it was 2 biological reads or one biological and one technical.
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
215
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
216 .. class:: warningmark
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
217
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
218 By default, only biological reads are dumped and in case of PAIRED dataset only the spots which have both reads will be in the paired-end collection. The remaining single reads will be in the other colletion.
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
219 To keep all reads, and maybe do not have the same number of reads in forward and reverse use the --split-files option in Advanced Options, Select how to split the spots.
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
220
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
221 @ACCESSION_LIST_HOWTO@
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
222
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
223 -----
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
224
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
225
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
226 .. _fastq: https://en.wikipedia.org/wiki/FASTQ_format
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
227 .. _fastq-dump: https://ncbi.github.io/sra-tools/fastq-dump.html
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
228 .. _fasterq-dump: https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
229 .. _collection: https://galaxyproject.org/tutorials/collections/
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
230 .. _link: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
231
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
232 @SRATOOLS_ATTRRIBUTION@
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
233
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
234 ]]>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
235 </help>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
236 <expand macro="citation"/>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
237 </tool>