Mercurial > repos > bgruening > diamond
comparison diamond.xml @ 7:62c9df8382c2 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
author | bgruening |
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date | Tue, 03 Dec 2019 17:40:05 -0500 |
parents | 64be1ac21109 |
children | 54f751e413f4 |
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6:64be1ac21109 | 7:62c9df8382c2 |
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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> |