| Previous changeset 29:6ea73833cf67 (2023-06-23) Next changeset 31:734abc7ac21d (2023-09-14) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787 |
|
modified:
fasterq_dump.xml fastq_dump.xml macros.xml |
| b |
| diff -r 6ea73833cf67 -r 4317d3cb6cba fasterq_dump.xml --- a/fasterq_dump.xml Fri Jun 23 21:32:08 2023 +0000 +++ b/fasterq_dump.xml Mon Sep 11 08:37:23 2023 +0000 |
| [ |
| @@ -14,7 +14,7 @@ @SET_ACCESSIONS@ while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1} - --seq-defline '@\$sn/\$ri' + --seq-defline '$adv.seq_defline' --qual-defline '+' $adv.split #if str( $adv.minlen ) != "": @@ -71,6 +71,7 @@ <inputs> <expand macro="input_conditional"/> <section name="adv" title="Advanced Options" expanded="False"> + <expand macro="defline" defline_param="--seq-defline" defline_default="@$sn/$ri"/> <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--min-read-len"/> <param name="split" type="select" display="radio" label="Select how to split the spots" help="This option will only be used when there are multiple reads per spot (for example paired-end)."> <option value="--split-3">--split-3: write properly paired biological reads into different files and single reads in another file</option> |
| b |
| diff -r 6ea73833cf67 -r 4317d3cb6cba fastq_dump.xml --- a/fastq_dump.xml Fri Jun 23 21:32:08 2023 +0000 +++ b/fastq_dump.xml Mon Sep 11 08:37:23 2023 +0000 |
| [ |
| @@ -22,7 +22,7 @@ fastq-dump --accession "\$acc" --split-files #end if - --defline-seq '@\$sn[_\$rn]/\$ri' + --defline-seq '$adv.defline_seq' --defline-qual '+' $adv.split @@ -91,6 +91,7 @@ <option value="fastqsanger.bz2">bzip2 compressed fastq</option> </param> <section name="adv" title="Advanced Options" expanded="False"> + <expand macro="defline" defline_param="--defline-seq" defline_default="@$sn[_$rn]/$ri"/> <param name="minID" type="integer" label="Minimum spot ID" optional="true" help="Minimum spot id to be dumped." argument="--minSpotId"/> <param name="maxID" type="integer" label="Maximum spot ID" optional="true" help="Maximum spot id to be dumped." argument="--maxSpotId"/> <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="--minReadLen"/> |
| b |
| diff -r 6ea73833cf67 -r 4317d3cb6cba macros.xml --- a/macros.xml Fri Jun 23 21:32:08 2023 +0000 +++ b/macros.xml Mon Sep 11 08:37:23 2023 +0000 |
| [ |
| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">3.0.5</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">22.01</token> <xml name="edam_ontology"> <edam_topics> @@ -123,6 +123,33 @@ <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true" help="Filter by distance between matepairs. Use unknown to find matepairs split between the references. Use from-to (inclusive) to limit matepair distance on the same reference" argument="--matepair-distance"/> </macro> + <macro name="defline" tokens="defline_param,defline_default"> + <param argument="@DEFLINE_PARAM@" value="@DEFLINE_DEFAULT@" type="text" label="Defline format specification for sequence"> + <help>A string of characters and/or variables. The variables can be one of: + $ac: accession, $si: spot id, $sn: spot name, $sg: spot group (barcode), $sl: spot length in bases, $ri: read number, $rn: read name, $rl: read length in bases. + '[]' could be used for an optional output: if all vars in [] yield empty values whole group is not printed. Empty value is empty string or for numeric variables. + Ex: @$sn[_$rn]/$ri '_$rn' is omitted if name is empty"</help> + <!-- allow many chars, but quotes and backslash --> + <sanitizer> + <valid initial="string.ascii_letters,string.digits"> + <add value="@" /> + <add value="$" /> + <add value="[" /> + <add value="]" /> + <add value="_" /> + <add value="-" /> + <add value="+" /> + <add value="." /> + <add value=";" /> + <add value=":" /> + <add value="/" /> + <add value="?" /> + </valid> + </sanitizer> + <validator type="regex" message="Must start with @">^.*</validator> + + </param> + </macro> <macro name="citation"> <citations> <citation type="doi">10.1093/nar/gkq1019</citation> |