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comparison fasterq_dump.xml @ 17:37f09413ddbf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
author iuc
date Mon, 08 Jun 2020 09:48:56 +0000
parents f61761f373ea
children c8d04fc889f2
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16:f61761f373ea 17:37f09413ddbf
1 <tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy2" profile="18.01"> 1 <tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy0" profile="18.01">
2 <description>format from NCBI SRA</description> 2 <description>format from NCBI SRA</description>
3 <macros> 3 <macros>
4 <import>sra_macros.xml</import> 4 <import>sra_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <version_command>fasterq-dump --version</version_command> 7 <version_command>fasterq-dump --version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @COPY_CONFIGFILE@
9 @SET_ACCESSIONS@ 10 @SET_ACCESSIONS@
10 #if $input.input_select == "file": 11 #if $input.input_select == "file":
11 acc='${input.file.name}' && 12 acc='${input.file.name}' &&
12 ln -s '${input.file}' "\$acc" && 13 ln -s '${input.file}' "\$acc" &&
13 #end if 14 #end if
14 @CONFIGURE_TIMEOUT@
15 @CONFIGURE_RETRY@ 15 @CONFIGURE_RETRY@
16 while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do 16 while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
17 fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1} 17 fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
18 $adv.split 18 $adv.split
19 #if str( $adv.minlen ) != "": 19 #if str( $adv.minlen ) != "":
20 --min-read-len "$adv.minlen" 20 --min-read-len "$adv.minlen"
21 #end if 21 #end if
22 $adv.skip_technical >> $log 2>&1 ; 22 $adv.skip_technical >> $log 2>&1 ;
23 if [ \$? == 0 ] ; then 23 if [ \$? == 0 ] && [ \$(ls *.fastq | wc -l) -ge 1 ]; then
24 break ; 24 break ;
25 else 25 else
26 echo "Prefetch attempt \$SRA_PREFETCH_ATTEMPT of \$SRA_PREFETCH_RETRIES exited with code \$?" ; 26 echo "Prefetch attempt \$SRA_PREFETCH_ATTEMPT of \$SRA_PREFETCH_RETRIES exited with code \$?" ;
27 SRA_PREFETCH_ATTEMPT=`expr \$SRA_PREFETCH_ATTEMPT + 1` ; 27 SRA_PREFETCH_ATTEMPT=`expr \$SRA_PREFETCH_ATTEMPT + 1` ;
28 sleep 1 ; 28 sleep 1 ;
29 fi ; 29 fi ;
30 done && 30 done &&
31 mkdir -p output && 31 mkdir -p output &&
32 mkdir -p outputOther && 32 mkdir -p outputOther &&
33 count=`ls *.fastq | wc -l` && 33 count="\$(ls *.fastq | wc -l)" &&
34 echo "There are \$count fastq" && 34 echo "There are \$count fastq" &&
35 data=(\$(ls *.fastq)) && 35 data=(\$(ls *.fastq)) &&
36 if [ "\$count" -eq 1 ]; then 36 if [ "\$count" -eq 1 ]; then
37 @COMPRESS@ "\${data[0]}" > output/"\${acc}"__single.fastqsanger.gz && 37 @COMPRESS@ "\${data[0]}" > output/"\${acc}"__single.fastqsanger.gz &&
38 rm "\${data[0]}"; 38 rm "\${data[0]}";
66 #elif $input.input_select=="accession_number": 66 #elif $input.input_select=="accession_number":
67 ); 67 );
68 #end if 68 #end if
69 ]]> 69 ]]>
70 </command> 70 </command>
71 <expand macro="configfile_hack"/>
71 <inputs> 72 <inputs>
72 <expand macro="input_conditional"/> 73 <expand macro="input_conditional"/>
73 <section name="adv" title="Advanced Options" expanded="False"> 74 <section name="adv" title="Advanced Options" expanded="False">
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"/> 75 <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"/>
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)."> 76 <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).">
234 235
235 .. _fastq: https://en.wikipedia.org/wiki/FASTQ_format 236 .. _fastq: https://en.wikipedia.org/wiki/FASTQ_format
236 .. _fastq-dump: https://ncbi.github.io/sra-tools/fastq-dump.html 237 .. _fastq-dump: https://ncbi.github.io/sra-tools/fastq-dump.html
237 .. _fasterq-dump: https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump 238 .. _fasterq-dump: https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump
238 .. _collection: https://galaxyproject.org/tutorials/collections/ 239 .. _collection: https://galaxyproject.org/tutorials/collections/
239 .. _link: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies 240 .. _link: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies
240 241
241 @SRATOOLS_ATTRRIBUTION@ 242 @SRATOOLS_ATTRRIBUTION@
242 243
243 ]]> 244 ]]>
244 </help> 245 </help>