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comparison diamond.xml @ 7:62c9df8382c2 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
author bgruening
date Tue, 03 Dec 2019 17:40:05 -0500
parents 64be1ac21109
children 54f751e413f4
comparison
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6:64be1ac21109 7:62c9df8382c2
1 <tool id="bg_diamond" name="Diamond" version="@VERSION@.0"> 1 <tool id="bg_diamond" name="Diamond" version="@VERSION@.0" profile="19.01">
2 <description>alignment tool for short sequences against a protein database</description> 2 <description>alignment tool for short sequences against a protein database</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
62 --id '$id' 62 --id '$id'
63 --query-cover '$query_cover' 63 --query-cover '$query_cover'
64 --subject-cover '$subject_cover' 64 --subject-cover '$subject_cover'
65 --block-size '$block_size' 65 --block-size '$block_size'
66 #if str($unal) == '1': 66 #if str($unal) == '1':
67 --unal 1 --un '$unalqueries' 67 --unal 1 --un '$unalqueries'
68 #end if 68 #end if
69 $no_self_hits 69 $no_self_hits
70 #if $tax_cond.tax_select == 'file': 70 #if $tax_cond.tax_select == 'file':
71 --taxonlist `cat '$tax_cond.taxonlistfile' | grep -v "^#" | grep -v "^$" | tr "\n" "," | sed 's/,$//'` 71 --taxonlist `cat '$tax_cond.taxonlistfile' | grep -v "^#" | grep -v "^$" | tr "\n" "," | sed 's/,$//'`
72 #else if $tax_cond.tax_select == 'list': 72 #else if $tax_cond.tax_select == 'list':
101 <option value="24">Pterobranchia Mitochondrial Code</option> 101 <option value="24">Pterobranchia Mitochondrial Code</option>
102 <option value="25">Candidate Division SR1 and Gracilibacteria Code</option> 102 <option value="25">Candidate Division SR1 and Gracilibacteria Code</option>
103 <option value="26">Pachysolen tannophilus Nuclear Code</option> 103 <option value="26">Pachysolen tannophilus Nuclear Code</option>
104 </param> 104 </param>
105 <param argument="--min-orf" name="min_orf" type="integer" value="1" label="ignore translated sequences without an open reading frame of at least this length" help="By default this feature is disabled for sequences of length below 30, set to 20 for sequences of length below 100, and set to 40 otherwise. Setting this option to 1 will disable this feature" /> 105 <param argument="--min-orf" name="min_orf" type="integer" value="1" label="ignore translated sequences without an open reading frame of at least this length" help="By default this feature is disabled for sequences of length below 30, set to 20 for sequences of length below 100, and set to 40 otherwise. Setting this option to 1 will disable this feature" />
106 106
107 <param name="query_strand" argument="--strand" type="select" label="query strands to search" help=""> 107 <param name="query_strand" argument="--strand" type="select" label="query strands to search" help="">
108 <option value="both" selected="True">Both</option> 108 <option value="both" selected="True">Both</option>
109 <option value="plus">Plus</option> 109 <option value="plus">Plus</option>
110 <option value="minus">Minus</option> 110 <option value="minus">Minus</option>
111 </param> 111 </param>
163 <param argument="--gapextend" type="integer" optional="True" value="" label="Gap extension penalty" help="leave empty for default (see scoring matrix)" /> 163 <param argument="--gapextend" type="integer" optional="True" value="" label="Gap extension penalty" help="leave empty for default (see scoring matrix)" />
164 <param name="comp_based_stats" argument="--comp-based-stats" type="boolean" truevalue="1" falsevalue="0" checked="true" label="enable composition based statistics?" help="Compositionally biased sequences often cause false positive matches, which are effectively filtered by this algorithm in a way similar to the composition based statistics used by BLAST"/> 164 <param name="comp_based_stats" argument="--comp-based-stats" type="boolean" truevalue="1" falsevalue="0" checked="true" label="enable composition based statistics?" help="Compositionally biased sequences often cause false positive matches, which are effectively filtered by this algorithm in a way similar to the composition based statistics used by BLAST"/>
165 <param argument="--masking" type="boolean" truevalue="1" falsevalue="0" checked="true" label="enable masking of low complexity regions?" help="Masked residues appear in the output as X"/> 165 <param argument="--masking" type="boolean" truevalue="1" falsevalue="0" checked="true" label="enable masking of low complexity regions?" help="Masked residues appear in the output as X"/>
166 <conditional name="tax_cond"> 166 <conditional name="tax_cond">
167 <param name="tax_select" type="select" label="Restrict search taxonomically?" help="Any taxonomic rank can be used, and only reference sequences matching one of the specified taxon ids will be searched against"> 167 <param name="tax_select" type="select" label="Restrict search taxonomically?" help="Any taxonomic rank can be used, and only reference sequences matching one of the specified taxon ids will be searched against">
168 <option value="no">No</option> 168 <option value="no" selected="True">No</option>
169 <option value="list">list of taxids entered manually</option> 169 <option value="list">list of taxids entered manually</option>
170 <option value="file">list of taxids from single column tabular file</option> 170 <option value="file">list of taxids from single column tabular file</option>
171 </param> 171 </param>
172 <when value="no"/> 172 <when value="no"/>
173 <when value="list"> 173 <when value="list">
177 <param name="taxonlistfile" argument="--taxonlist" type="data" format="tabular" label="Keep alignments within the given percentage range of the top alignment score for a quer" help="" /> 177 <param name="taxonlistfile" argument="--taxonlist" type="data" format="tabular" label="Keep alignments within the given percentage range of the top alignment score for a quer" help="" />
178 </when> 178 </when>
179 </conditional> 179 </conditional>
180 <conditional name="filter_score"> 180 <conditional name="filter_score">
181 <param name="filter_score_select" type="select" label="Method to filter?" help="(--evalue/--min-score)"> 181 <param name="filter_score_select" type="select" label="Method to filter?" help="(--evalue/--min-score)">
182 <option value="evalue">Maximum e-value to report alignments</option> 182 <option value="evalue" selected="True">Maximum e-value to report alignments</option>
183 <option value="min-score">Minimum bit score to report alignments</option> 183 <option value="min-score">Minimum bit score to report alignments</option>
184 </param> 184 </param>
185 <when value="evalue"> 185 <when value="evalue">
186 <param argument="--evalue" type="float" value="0.001" label="Maximum expected value to keep an alignment" /> 186 <param argument="--evalue" type="float" value="0.001" label="Maximum expected value to keep an alignment" />
187 </when> 187 </when>