Mercurial > repos > iuc > biotradis
changeset 5:8e4a4f240961 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 5aac8c4c9990e8796c8a4c55d6c900c03e6db3c0
| author | iuc |
|---|---|
| date | Wed, 13 Mar 2024 14:56:52 +0000 |
| parents | d1855ded740a |
| children | |
| files | bacteria_tradis.xml macros.xml tradis_essentiality.xml tradis_gene_insert_sites.xml |
| diffstat | 4 files changed, 24 insertions(+), 14 deletions(-) [+] |
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--- a/bacteria_tradis.xml Mon Jul 04 07:29:27 2022 +0000 +++ b/bacteria_tradis.xml Wed Mar 13 14:56:52 2024 +0000 @@ -3,6 +3,7 @@ <macros> <import>macros.xml</import> </macros> + <expand macro="xrefs"/> <expand macro="requirements" /> <command detect_errors="aggressive"> <![CDATA[ @@ -25,6 +26,7 @@ #if str($tranposon_tag.use) == "yes": -m '$tranposon_tag.nb_mismatches' -t '$tranposon_tag.sequence' + -td '$tranposon_tag.tagdir' #end if 2>&1 ]]> @@ -43,13 +45,15 @@ <when value="modify"> <conditional name="set_kmers_options"> - <param name="set" type="boolean" label="Modify kmers parameters" truevalue='yes' falsevalue='no' /> + <param name="set" type="select" label="Modify kmers parameters"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> <when value="yes"> - <param name="kmer_length" type="integer" value="" min="9" max="20" label=" Length of kmers hashed (--smalt_k)" help=" The minimum length of an exact match between a read and the genome needed to trigger an alignment attempt. Appropriate values are between ~10 and 20 for bacterial genomes depending on read length. Lower values lead to increased sensitivity at the expense of runtime." /> - <param name="step_size" type="integer" value="" min="1" max="15" label="Step size for smalt kmers (--smalt_s)" help=" Distance between the start of hashed kmers. Appropriate values are between 1 and ~15, but should be less than --smalt_k to ensure kmers overlap. Lower values lead to increased sensitivity at the expense of runtime." /> - </when> - <when value="no"> - </when> + <param name="kmer_length" type="integer" value="" min="9" max="20" label="Length of kmers hashed (--smalt_k)" help=" The minimum length of an exact match between a read and the genome needed to trigger an alignment attempt. Appropriate values are between ~10 and 20 for bacterial genomes depending on read length. Lower values lead to increased sensitivity at the expense of runtime." /> + <param name="step_size" type="integer" value="" min="1" max="15" label="Step size for smalt kmers (--smalt_s)" help=" Distance between the start of hashed kmers. Appropriate values are between 1 and ~15, but should be less than --smalt_k to ensure kmers overlap. Lower values lead to increased sensitivity at the expense of runtime." /> + </when> + <when value="no"/> </conditional> <param name="min_percentage" type="float" value="0.96" min="0" max="1" label="Minimum percentage of identical bases between read and reference (--smalt_y)" help="May be lowered to improve sensitivity in the case of low quality or short reads." /> @@ -62,20 +66,19 @@ </conditional> <conditional name="tranposon_tag"> - <param name="use" type="boolean" truevalue="yes" falsevalue="no" label="Search for a tranposon tag" help="Use with data containing a transposon tag attached to the reads. Only reads containing the transposon tag will be processed, and the tag will be removed before mapping." /> - + <param name="use" type="select" label="Search for a tranposon tag" help="Use with data containing a transposon tag attached to the reads. Only reads containing the transposon tag will be processed, and the tag will be removed before mapping."> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> <when value="yes"> - <param name="sequence" type="text" value="" help="" /> <param name="nb_mismatches" type="integer" value="2" min="0" help="If there is evidence for low-quality bases in the transposon tag (from FastQC, for instance), setting this to 1 or 2 may result in higher recovery of insertion sites. Higher than 2 is not advisable with the typical transposon tag lengths (10 - 12 bases) produced by TraDIS protocols, but may be appropriate with protocols that produce significantly longer transposon tags." /> <param name="tagdir" type="select" label="Direction of the transposon tag" help="" > <option value="3" selected="true">3'</option> - <option value="5">5bacteria_tradis.xml'</option> + <option value="5">5'</option> </param> - </when> - <when value="no"> - </when> + <when value="no"/> </conditional>
--- a/macros.xml Mon Jul 04 07:29:27 2022 +0000 +++ b/macros.xml Wed Mar 13 14:56:52 2024 +0000 @@ -1,12 +1,17 @@ <?xml version="1.0"?> <macros> - <token name="@VERSION@">2</token> + <token name="@VERSION@">3</token> <token name="@TOOL_VERSION@">1.4.5</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">biotradis</requirement> </requirements> </xml> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">biotradis</xref> + </xrefs> + </xml> <xml name="citations"> <citations> <citation type="doi">10.1093/bioinformatics/btw022</citation>