Mercurial > repos > p.lucas > diamond_using_binary
changeset 4:c07dbfd76866 draft
Uploaded macros
author | p.lucas |
---|---|
date | Tue, 28 May 2024 12:54:16 +0000 |
parents | de64f8ab4878 |
children | 58b3c7726a1a |
files | macros.xml |
diffstat | 1 files changed, 173 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue May 28 12:54:16 2024 +0000 @@ -0,0 +1,173 @@ +<macros> + <token name="@TOOL_VERSION@">2.1.9</token> + <token name="@VERSION_SUFFIX@">0</token> + + <xml name="stdio"> + <stdio> + <regex match="Failed to allocate" source="stderr" level="fatal_oom" /> + </stdio> + </xml> + + <xml name="version_command"> + <version_command>/usr/bin/diamond version | cut -d" " -f 3</version_command> + </xml> + + <xml name="output_type_macro"> + <conditional name="output"> + <param argument="--outfmt" type="select" label="Format of output file" help=""> + <option value="0">BLAST pairwise</option> + <option value="5">BLAST XML</option> + <option value="6">BLAST tabular</option> + <option value="100">DAA</option> + <option value="101">SAM</option> + <option value="102">Taxonomic classification</option> + </param> + <when value="0"/> + <when value="5"/> + <when value="6"> + <param name="fields" type="select" label="Tabular fields" help="" multiple="true"> + <option value="qseqid" selected="true">Query Seq - id</option> + <option value="sseqid" selected="true">Subject Seq - id</option> + <option value="sallseqid">All subject Seq - id(s)</option> + <option value="qlen">Query sequence length</option> + <option value="slen">Subject sequence length</option> + <option value="pident" selected="true">Percentage of identical matches</option> + <option value="length" selected="true">Alignment length</option> + <option value="nident">Number of identical matches</option> + <option value="mismatch" selected="true">Number of mismatches</option> + <option value="positive">Number of positive - scoring matches</option> + <option value="gapopen" selected="true">Number of gap openings</option> + <option value="gaps">Total number of gaps</option> + <option value="ppos">Percentage of positive - scoring matches</option> + <option value="qstart" selected="true">Start of alignment in query</option> + <option value="qend" selected="true">End of alignment in query</option> + <option value="sstart" selected="true">Start of alignment in subject</option> + <option value="send" selected="true">End of alignment in subject</option> + <option value="qseq">Aligned part of query sequence</option> + <option value="sseq">Aligned part of subject sequence</option> + <option value="qseq_translated">Translation of the aligned part of query sequence</option> + <option value="evalue" selected="true">Expect value</option> + <option value="bitscore" selected="true">Bit score</option> + <option value="score">Raw score</option> + <option value="qframe">Query frame</option> + <option value="btop">Blast traceback operations(BTOP)</option> + <option value="scovhsp">Subject coverage per HSP</option> + <option value="stitle">Subject Title</option> + <option value="salltitles">All Subject Title(s)</option> + <option value="qcovhsp">Query Coverage Per HSP</option> + <option value="qtitle">Query title</option> + <option value="full_qseq">Query sequence</option> + <option value="full_sseq">Subject sequence</option> + <option value="qqual">Query quality values for the aligned part of the query</option> + <option value="full_qqual">Query quality values</option> + <option value="qstrand">Query strand</option> + <option value="cigar">Cigar</option> + <yield/> + </param> + <param argument="--unal" type="boolean" label="Report unaligned queries" truevalue="1" falsevalue="0" checked="false"/> + </when> + <when value="100"> + <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/> + <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/> + </when> + <when value="101"> + <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/> + <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/> + </when> + <when value="102"/> + </conditional> + </xml> + + <xml name="hit_filter_macro"> + <conditional name="hit_filter"> + <param name="hit_filter_select" type="select" label="Method to restrict the number of hits?"> + <option value="max">Maximum number of target sequences</option> + <option value="top">Percentage of top alignment score</option> + </param> + <when value="max"> + <param name="max_target_seqs" argument="--max-target-seqs" type="integer" value="25" label="The maximum number of target sequences per query to report alignments for" + help="Setting this to 0 will report all alignments that were found." /> + </when> + <when value="top"> + <param argument="--top" type="integer" value="0" label="Keep alignments within the given percentage range of the top alignment score for a query" + help="For example, setting this to 10 will report all alignments whose score is at most 10% lower than the best alignment score for a query." /> + </when> + </conditional> + </xml> + + <xml name="block_size_low_sens"> + <param argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time" + help="This is the main parameter for controlling the program’s memory and disk space usage. Bigger numbers will increase the use of memory and temporary + disk space, but also improve performance" /> + </xml> + + <xml name="block_size_hi_sens"> + <param argument="--block-size" type="float" value="0.4" label="Block size in billions of sequence letters to be processed at a time" + help="This is the main parameter for controlling the program’s memory and disk space usage. Bigger numbers will increase the use of memory and temporary + disk space, but also improve performance" /> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nmeth.3176</citation> + </citations> + </xml> + + + <xml name="output_macro"> + <data format="txt" name="blast_pairw" label="${tool.name} on ${on_string}"> + <filter>output_section["output"]["outfmt"] == "0"</filter> + </data> + <data format="xml" name="blast_xml" label="${tool.name} on ${on_string}"> + <filter>output_section["output"]["outfmt"] == "5"</filter> + </data> + <data format="tabular" name="blast_tabular" label="${tool.name} on ${on_string}"> + <filter>output_section["output"]["outfmt"] == "6"</filter> + </data> + <!-- for daa diamond appends the .daa extension -> hence from_work_dir --> + <data format="daa" name="daa_output" label="${tool.name} on ${on_string}" from_work_dir="output.daa"> + <filter>output_section["output"]["outfmt"] == "100"</filter> + </data> + <data format="sam" name="sam_output" label="${tool.name} on ${on_string}"> + <filter>output_section["output"]["outfmt"] == "101"</filter> + </data> + <data format="tabular" name="tax_output" label="${tool.name} on ${on_string}"> + <filter>output_section["output"]["outfmt"] == "102"</filter> + </data> + </xml> + + <token name="@OUTPUT_ARGS@"> + #if $output_section.output.outfmt == "0" + --outfmt '0' + --out '$blast_pairw' + #else if $output_section.output.outfmt == "5" + --outfmt '5' + --out '$blast_xml' + #else if $output_section.output.outfmt == "6" + --outfmt '6' #echo ' '.join(str($output_section.output.fields).split(',')) + --out '$blast_tabular' + --unal $output_section.output.unal + #else if $output_section.output.outfmt == "100" + --outfmt '100' + $output_section.output.salltitles + $output_section.output.sallseqid + --out output.daa + #else if $output_section.output.outfmt == "101" + --outfmt '101' + $output_section.output.salltitles + $output_section.output.sallseqid + --out '$sam_output' + #else if $output_section.output.outfmt == "102" + --outfmt '102' + --out '$tax_output' + #end if + </token> + + <token name="@HITFILTER_ARGS@"> + #if str($hit_filter.hit_filter_select) == 'max': + --max-target-seqs '$hit_filter.max_target_seqs' + #else: + --top '$hit_filter.top' + #end if + </token> +</macros>