Mercurial > repos > iuc > sra_tools

annotate fasterq_dump.xml @ 23:6669afa92957 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 cbb1499906c801443d72bdf313d86f0182aca010
author iuc
date Sun, 22 Jan 2023 17:51:28 +0000
parents fe99dc15b7af
children f7732611d0fc
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
1 <tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
2 <description>format from NCBI SRA</description>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
3 <macros>
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
4 <import>macros.xml</import>
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
5 </macros>
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
6 <expand macro="edam_ontology"/>
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
7 <expand macro="bio_tools"/>
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
8 <expand macro="requirements"/>
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
9 <version_command>fasterq-dump --version | tr -d $'\n'</version_command>
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
20
b50c21c6e6bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 3c5c7587a9e8f4177db5ff1390b7e29cb190eb72"
iuc
parents: 19
diff changeset
11 set -o | grep -q pipefail && set -o pipefail;
17
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
iuc
parents: 16
diff changeset
12 @COPY_CONFIGFILE@
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
13 @CONFIGURE_RETRY@
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
14 @SET_ACCESSIONS@
16
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
15 while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
22
fe99dc15b7af "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 21f935ba50d3e4b455246c681e54d5c57c67032f"
iuc
parents: 21
diff changeset
16 fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
17 --seq-defline '@\$sn/\$ri'
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
18 --qual-defline '+'
16
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
19 $adv.split
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
20 #if str( $adv.minlen ) != "":
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
21 --min-read-len "$adv.minlen"
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
22 #end if
21
9828888fc245 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
iuc
parents: 20
diff changeset
23 $adv.skip_technical 2>&1 | tee -a '$log';
17
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
iuc
parents: 16
diff changeset
24 if [ \$? == 0 ] && [ \$(ls *.fastq | wc -l) -ge 1 ]; then
16
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
25 break ;
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
26 else
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
27 echo "Prefetch attempt \$SRA_PREFETCH_ATTEMPT of \$SRA_PREFETCH_RETRIES exited with code \$?" ;
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
28 SRA_PREFETCH_ATTEMPT=`expr \$SRA_PREFETCH_ATTEMPT + 1` ;
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
29 sleep 1 ;
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
30 fi ;
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
31 done &&
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
32 mkdir -p output &&
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
33 mkdir -p outputOther &&
17
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
iuc
parents: 16
diff changeset
34 count="\$(ls *.fastq | wc -l)" &&
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
35 echo "There are \$count fastq files" &&
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
36 data=(\$(ls *.fastq)) &&
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
37 if [ "\$count" -eq 1 ]; then
16
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
38 @COMPRESS@ "\${data[0]}" > output/"\${acc}"__single.fastqsanger.gz &&
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
39 rm "\${data[0]}";
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
40 elif [ "$adv.split" = "--split-3" ]; then
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
41 if [ -e "\${acc}".fastq ]; then
16
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
42 @COMPRESS@ "\${acc}".fastq > outputOther/"\${acc}"__single.fastqsanger.gz;
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
43 fi &&
16
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
44 @COMPRESS@ "\${acc}"_1.fastq > output/"\${acc}"_forward.fastqsanger.gz &&
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
45 @COMPRESS@ "\${acc}"_2.fastq > output/"\${acc}"_reverse.fastqsanger.gz &&
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
46 rm "\${acc}"*.fastq;
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
47 elif [ "\$count" -eq 2 ]; then
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
48 #if $adv.skip_technical:
16
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
49 @COMPRESS@ "\${data[0]}" > output/"\${acc}"_forward.fastqsanger.gz &&
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
50 @COMPRESS@ "\${data[1]}" > output/"\${acc}"_reverse.fastqsanger.gz &&
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
51 #else
16
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
52 @COMPRESS@ "\${data[0]}" > outputOther/"\${data[0]}"sanger.gz &&
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
53 @COMPRESS@ "\${data[1]}" > outputOther/"\${data[1]}"sanger.gz &&
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
54 #end if
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
55 rm "\${data[0]}" &&
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
56 rm "\${data[1]}";
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
57 else
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
58 for file in \${data[*]}; do
16
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
59 @COMPRESS@ "\$file" > outputOther/"\$file"sanger.gz &&
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
60 rm "\$file";
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
61 done;
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
62 fi;
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
63
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
64 #if $input.input_select != "sra_file":
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
65 ); done;
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
66 #end if
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
67 echo "Done with all accessions."
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
68 ]]>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
69 </command>
17
37f09413ddbf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
iuc
parents: 16
diff changeset
70 <expand macro="configfile_hack"/>
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
71 <inputs>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
72 <expand macro="input_conditional"/>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
73 <section name="adv" title="Advanced Options" expanded="False">
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
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"/>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
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).">
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
76 <option value="--split-3">--split-3: write properly paired biological reads into different files and single reads in another file</option>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
77 <option value="--split-files">--split-files: write reads into different files (forward and reverse may not match if one read is empty)</option>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
78 <option value="--split-spot">--split-spot: split spots into reads (only one output file)</option>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
79 <option value="--concatenate-reads">--concatenate-reads: writes whole spots into one file</option>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
80 </param>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
81 <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"/>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
82 </section>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
83 </inputs>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
84 <outputs>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
85 <data name="log" format="txt" label="fasterq-dump log"/>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
86 <collection name="list_paired" type="list:paired" label="Pair-end data (fasterq-dump)">
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
87
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
88 <!-- Use named regex group to grab pattern
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
89 <identifier_0>_<identifier_1>.fq. Here identifier_0 is the list
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
90 identifier in the nested collection and identifier_1 is either
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
91 forward or reverse (for instance samp1_forward.fq).
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
92 -->
16
f61761f373ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 15
diff changeset
93
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
94 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastqsanger.gz" directory="output" ext="fastqsanger.gz" />
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
95 </collection>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
96 <collection name="output_collection" type='list' label="Single-end data (fasterq-dump)">
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
97 <discover_datasets pattern="(?P&lt;designation&gt;.+)__single\.fastqsanger.gz" directory="output" ext='fastqsanger.gz'/>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
98 </collection>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
99 <collection name="output_collection_other" type='list' label="Other data (fasterq-dump)">
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
100 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fastqsanger\.gz" directory="outputOther" format="fastqsanger.gz"/>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
101 </collection>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
102 </outputs>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
103 <tests>
21
9828888fc245 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
iuc
parents: 20
diff changeset
104 <test expect_num_outputs="4">
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
105 <param name="input_select" value="accession_number"/>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
106 <param name="accession" value="ERR086330"/>
21
9828888fc245 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
iuc
parents: 20
diff changeset
107 <output_collection name="list_paired" type="list:paired" count="1">
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
108 <element name="ERR086330">
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
109 <element name="forward" file="ERR086330_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
110 <element name="reverse" file="ERR086330_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
111 </element>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
112 </output_collection>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
113 </test>
21
9828888fc245 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
iuc
parents: 20
diff changeset
114 <test expect_num_outputs="4">
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
115 <param name="input_select" value="accession_number"/>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
116 <param name="accession" value="SRR002702"/>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
117 <param name="split" value="--split-files"/>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
118 <param name="skip_technical" value="False"/>
21
9828888fc245 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
iuc
parents: 20
diff changeset
119 <output_collection name="output_collection_other" type="list" count="2">
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
120 <element name="SRR002702_1" file="SRR002702_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
121 <element name="SRR002702_2" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
122 </output_collection>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
123 </test>
21
9828888fc245 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
iuc
parents: 20
diff changeset
124 <test expect_num_outputs="4">
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
125 <param name="input_select" value="accession_number"/>
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
126 <param name="accession" value="ERR086330, SRR11953971"/>
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
127 <output_collection name="list_paired" type="list:paired" count="2">
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
128 <element name="ERR086330">
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
129 <element name="forward" file="ERR086330_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
130 <element name="reverse" file="ERR086330_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
131 </element>
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
132 <element name="SRR11953971">
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
133 <element name="forward" file="SRR11953971_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
134 <element name="reverse" file="SRR11953971_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
135 </element>
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
136 </output_collection>
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
137 </test>
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
138 <test expect_num_outputs="4">
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
139 <param name="input_select" value="sra_file"/>
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
140 <param name="sra_file" value="SRR522874.sra"/>
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
141 <param name="split" value="--split-files"/>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
142 <param name="skip_technical" value="True"/>
21
9828888fc245 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
iuc
parents: 20
diff changeset
143 <output_collection name="list_paired" type="list:paired" count="1">
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
144 <element name="SRR522874.sra">
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
145 <element name="forward" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
146 <element name="reverse" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
147 </element>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
148 </output_collection>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
149 </test>
21
9828888fc245 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
iuc
parents: 20
diff changeset
150 <test expect_num_outputs="4">
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
151 <param name="input_select" value="sra_file"/>
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
152 <param name="sra_file" value="SRR522874.sra"/>
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
153 <param name="split" value="--split-files"/>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
154 <param name="skip_technical" value="False"/>
21
9828888fc245 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
iuc
parents: 20
diff changeset
155 <output_collection name="output_collection_other" type="list" count="4">
9828888fc245 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
iuc
parents: 20
diff changeset
156 <element name="SRR522874_1" file="SRR522874.sra_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
9828888fc245 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
iuc
parents: 20
diff changeset
157 <element name="SRR522874_2" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
9828888fc245 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
iuc
parents: 20
diff changeset
158 <element name="SRR522874_3" file="SRR522874.sra_3.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
9828888fc245 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
iuc
parents: 20
diff changeset
159 <element name="SRR522874_4" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
160 </output_collection>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
161 </test>
21
9828888fc245 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
iuc
parents: 20
diff changeset
162 <test expect_num_outputs="4">
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
163 <param name="input_select" value="file_list"/>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
164 <param name="file_list" value="list_sra"/>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
165 <param name="minlen" value="21"/>
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
166 <output_collection name="output_collection_other" type="list" count="1">
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
167 <element name="SRR522874__single" file="SRR522874.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
168 </output_collection>
21
9828888fc245 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
iuc
parents: 20
diff changeset
169 <output_collection name="list_paired" type="list:paired" count="1">
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
170 <element name="SRR522874">
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
171 <element name="forward" file="SRR522874_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
172 <element name="reverse" file="SRR522874_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
173 </element>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
174 </output_collection>
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
175 <output_collection name="output_collection" type="list" count="1">
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
176 <element name="SRR002702" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
177 </output_collection>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
178 </test>
21
9828888fc245 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
iuc
parents: 20
diff changeset
179 <test expect_num_outputs="4">
18
c8d04fc889f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2646cabeb93bb9780c5c31839ea3189391b9a266"
iuc
parents: 17
diff changeset
180 <param name="input_select" value="file_list"/>
c8d04fc889f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2646cabeb93bb9780c5c31839ea3189391b9a266"
iuc
parents: 17
diff changeset
181 <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
21
9828888fc245 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
iuc
parents: 20
diff changeset
182 <output_collection name="list_paired" type="list:paired" count="1">
18
c8d04fc889f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2646cabeb93bb9780c5c31839ea3189391b9a266"
iuc
parents: 17
diff changeset
183 <element name="SRR11953971">
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
184 <element name="forward" file="SRR11953971_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
185 <element name="reverse" file="SRR11953971_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
18
c8d04fc889f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2646cabeb93bb9780c5c31839ea3189391b9a266"
iuc
parents: 17
diff changeset
186 </element>
c8d04fc889f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2646cabeb93bb9780c5c31839ea3189391b9a266"
iuc
parents: 17
diff changeset
187 </output_collection>
c8d04fc889f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2646cabeb93bb9780c5c31839ea3189391b9a266"
iuc
parents: 17
diff changeset
188 </test>
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
189 </tests>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
190 <help><![CDATA[
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
191 **What it does?**
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
192
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
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:
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
194
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
195 - if data is paired-ended (or mate-pair) the tool will generate a collection of file pairs, in which each element will be a pair of fastq_ files containing forward and reverse mates.
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
196 - if data is single ended, each element of the collection will be a single fastq_ dataset.
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
197
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
198
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
199 @HOW_TO_USE_IT@
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
200
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
201 -----
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
202
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
203 **Output**
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
204
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
205 In every case, fastq datasets produced will be saved in Galaxy's history as a collection_ - a single history element containing multiple datasets. In fact, regardless of the experimental design, 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.
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
206 Some collections may be empty if the accessions provided in the list do not contain one of the type of data.
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
207
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
208 .. class:: warningmark
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
209
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
210 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.
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
211
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
212 .. class:: warningmark
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
213
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
214 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.
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
215 To keep all reads, and potentially 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.
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
216
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
217 @ACCESSION_LIST_HOWTO@
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
218
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
219 -----
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
220
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
221
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
222 .. _fastq: https://en.wikipedia.org/wiki/FASTQ_format
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
223 .. _fasterq-dump: https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
224 .. _collection: https://galaxyproject.org/tutorials/collections/
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
225 .. _link: https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&display=reads
15
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
226
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
227 @SRATOOLS_ATTRRIBUTION@
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
228 ]]>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
229 </help>
54366e4d692a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
iuc
parents:
diff changeset
230 <expand macro="citation"/>
23
6669afa92957 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents: 22
diff changeset
231 </tool>