Mercurial > repos > iuc > sra_tools

annotate fasterq_dump.xml @ 23:653e89d73fc4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 3c5c7587a9e8f4177db5ff1390b7e29cb190eb72"
author iuc
date Thu, 20 Aug 2020 05:06:27 -0400
parents 751a694ec620
children e08a7ad4378b
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653e89d73fc4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 3c5c7587a9e8f4177db5ff1390b7e29cb190eb72"
iuc
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1 <tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy0" profile="18.01">
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2 <description>format from NCBI SRA</description>
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3 <macros>
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4 <import>sra_macros.xml</import>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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5 </macros>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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6 <expand macro="requirements"/>
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7 <version_command>fasterq-dump --version</version_command>
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8 <command detect_errors="exit_code"><![CDATA[
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9 set -o | grep -q pipefail && set -o pipefail;
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10 @COPY_CONFIGFILE@
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11 @SET_ACCESSIONS@
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12 #if $input.input_select == "file":
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13 acc='${input.file.name}' &&
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14 ln -s '${input.file}' "\$acc" &&
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15 #end if
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16 @CONFIGURE_RETRY@
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17 while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
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18 fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
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19 $adv.split
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20 #if str( $adv.minlen ) != "":
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21 --min-read-len "$adv.minlen"
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22 #end if
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23 $adv.skip_technical 2>&1 | tee $log;
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24 if [ \$? == 0 ] && [ \$(ls *.fastq | wc -l) -ge 1 ]; then
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25 break ;
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26 else
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27 echo "Prefetch attempt \$SRA_PREFETCH_ATTEMPT of \$SRA_PREFETCH_RETRIES exited with code \$?" ;
c441583adae5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
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28 SRA_PREFETCH_ATTEMPT=`expr \$SRA_PREFETCH_ATTEMPT + 1` ;
c441583adae5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
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29 sleep 1 ;
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30 fi ;
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31 done &&
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32 mkdir -p output &&
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33 mkdir -p outputOther &&
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34 count="\$(ls *.fastq | wc -l)" &&
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35 echo "There are \$count fastq" &&
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36 data=(\$(ls *.fastq)) &&
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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37 if [ "\$count" -eq 1 ]; then
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38 @COMPRESS@ "\${data[0]}" > output/"\${acc}"__single.fastqsanger.gz &&
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39 rm "\${data[0]}";
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
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40 elif [ "$adv.split" = "--split-3" ]; then
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41 if [ -e "\${acc}".fastq ]; then
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42 @COMPRESS@ "\${acc}".fastq > outputOther/"\${acc}"__single.fastqsanger.gz;
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43 fi &&
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44 @COMPRESS@ "\${acc}"_1.fastq > output/"\${acc}"_forward.fastqsanger.gz &&
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45 @COMPRESS@ "\${acc}"_2.fastq > output/"\${acc}"_reverse.fastqsanger.gz &&
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46 rm "\${acc}"*.fastq;
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47 elif [ "\$count" -eq 2 ]; then
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48 #if $adv.skip_technical:
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49 @COMPRESS@ "\${data[0]}" > output/"\${acc}"_forward.fastqsanger.gz &&
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50 @COMPRESS@ "\${data[1]}" > output/"\${acc}"_reverse.fastqsanger.gz &&
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51 #else
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52 @COMPRESS@ "\${data[0]}" > outputOther/"\${data[0]}"sanger.gz &&
c441583adae5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
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53 @COMPRESS@ "\${data[1]}" > outputOther/"\${data[1]}"sanger.gz &&
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54 #end if
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55 rm "\${data[0]}" &&
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56 rm "\${data[1]}";
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57 else
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58 for file in \${data[*]}; do
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59 @COMPRESS@ "\$file" > outputOther/"\$file"sanger.gz &&
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60 rm "\$file";
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61 done;
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62 fi;
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63 #if $input.input_select=="file_list":
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64 ) ; done
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65
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66 ;
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67 #elif $input.input_select=="accession_number":
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68 );
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69 #end if
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70 ]]>
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71 </command>
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72 <expand macro="configfile_hack"/>
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73 <inputs>
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74 <expand macro="input_conditional"/>
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75 <section name="adv" title="Advanced Options" expanded="False">
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76 <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"
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77 <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"
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78 <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"
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79 <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
80 <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
81 <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:
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82 </param>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
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83 <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:
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84 </section>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
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85 </inputs>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
86 <outputs>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
87 <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:
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88 <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:
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89
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
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90 <!-- 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
91 <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:
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92 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
93 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:
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94 -->
17
c441583adae5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
iuc
parents: 16
diff changeset
95
15
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
96 <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:
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97 </collection>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
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98 <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
99 <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:
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100 </collection>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
101 <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
102 <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:
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103 </collection>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
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104 </outputs>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
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105 <tests>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
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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 <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
108 <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:
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109 <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
110 <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
111 <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
112 </element>
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="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:
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114 </element>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
115 </element>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
116 </output_collection>
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:
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118 <test>
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="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
120 <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
121 <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
122 <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
123 <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
124 <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
125 <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
126 </output_collection>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
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127 </test>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
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128 <test>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
129 <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:
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130 <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
131 <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:
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132 <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:
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133 <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
134 <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
135 <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
136 </element>
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="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
138 </element>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
139 </element>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
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140 </output_collection>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
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141 </test>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
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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 <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:
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144 <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
145 <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
146 <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
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.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:
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149 <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
150 <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
151 <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
152 </output_collection>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
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153 </test>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
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154 <test>
f5ea3ce9b9b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
parents:
diff changeset
155 <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
156 <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:
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157 <param name="minlen" value="21"/>
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158 <output_collection name="output_collection_other" type="list">
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159 <element name="SRR522874__single" file="SRR522874.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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160 </output_collection>
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161 <output_collection name="list_paired" type="list:paired">
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162 <element name="SRR522874">
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163 <element name="forward" file="SRR522874_1.fastq.gz" decompress="True">
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164 </element>
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165 <element name="reverse" file="SRR522874_2.fastq.gz" decompress="True">
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166 </element>
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167 </element>
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168 </output_collection>
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169 <output_collection name="output_collection" type="list">
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170 <element name="SRR002702" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
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171 </output_collection>
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172 </test>
19
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173 <test>
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174 <param name="input_select" value="file_list"/>
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175 <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
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176 <output_collection name="list_paired" type="list:paired">
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177 <element name="SRR11857975">
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178 <element name="forward" file="SRR11857975_1.fastq.gz" decompress="True">
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179 </element>
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180 <element name="reverse" file="SRR11857975_2.fastq.gz" decompress="True">
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181 </element>
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182 </element>
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183 </output_collection>
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184 </test>
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185 <test>
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186 <param name="input_select" value="file_list"/>
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187 <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
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188 <output_collection name="list_paired" type="list:paired">
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189 <element name="SRR11953971">
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190 <element name="forward" file="SRR11953971_1.fastq.gz" decompress="True"/>
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191 <element name="reverse" file="SRR11953971_2.fastq.gz" decompress="True"/>
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192 </element>
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193 </output_collection>
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194 </test>
15
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195 </tests>
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196 <help><![CDATA[
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197 **What it does?**
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198
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199 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.
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200
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201 **How to use it?**
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202
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203 There are three ways in which you can download data:
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204
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205 1. Data for single accession
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206 2. Multiple datasets using a list of accessions
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207 3. Extract data from already uploaded SRA dataset
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208
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209 Below we discuss each in detail.
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210
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211 ------
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212
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213 **Uploading data for a single accession**
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214
17
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215 When you type a single accession number (e.g., `SRR1582967`) into **Accession** box and click **Execute** the tool will fetch data for you.
15
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216
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217 -----
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218
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219 **Uploading multiple datasets using a list of accessions**
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220
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221 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:
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222
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223 1. Upload it into your history using Galaxy's upload tool
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224 2. Once the list of accessions is uploaded choose *List of SRA accessions, one per line* from **select input type** dropdown
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225 3. Choose uploaded file within the **sra accession list** field
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226 4. Click **Execute**
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227
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228 -----
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229
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230 **Extract data from already uploaded SRA dataset**
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231
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232 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:
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233
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234 - 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).
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235 - if data is single ended, a standard fastq dataset will be produced
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236
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237 -----
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238
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239 **Output**
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240
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241 In every case, fastq datasets produced will be saved in Galaxy's history as a collection_ - a single history element containing multiple datasets.
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242 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"
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243 Some collections may be empty if the accessions provided in the list does not contain one of the type of data.
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245 .. class:: warningmark
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247 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.
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248
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249 .. class:: warningmark
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250
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251 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.
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252 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.
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254 @ACCESSION_LIST_HOWTO@
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256 -----
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257
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258
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259 .. _fastq: https://en.wikipedia.org/wiki/FASTQ_format
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260 .. _fastq-dump: https://ncbi.github.io/sra-tools/fastq-dump.html
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261 .. _fasterq-dump: https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump
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262 .. _collection: https://galaxyproject.org/tutorials/collections/
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263 .. _link: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies
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265 @SRATOOLS_ATTRRIBUTION@
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267 ]]>
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268 </help>
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269 <expand macro="citation"/>
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270 </tool>