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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 58fa50696846c7f6a5bcfc22a59243c80107e41a
author iuc
date Sat, 27 Jan 2024 23:29:55 +0000
parents 9f23fe0cb70b
children
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1:9f23fe0cb70b 2:92b9fd5f1f9f
1 <tool id="snipit" name="snipit" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="snipit" name="snipit" version="@TOOL_VERSION@+galaxy0">
2 <description>Summarise snps relative to a reference sequence</description> 2 <description>Summarise snps relative to a reference sequence</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.0.7</token> 4 <token name="@TOOL_VERSION@">1.2</token>
5 <xml name="handle_background" tokens="format"> 5 <xml name="handle_background" tokens="format">
6 <when value="@FORMAT@"> 6 <when value="@FORMAT@">
7 <param argument="--solid-background" name="transparent_background" type="boolean" truevalue="" falsevalue="--solid-background" label="Plot on transparent background?" /> 7 <param argument="--solid-background" name="transparent_background" type="boolean" truevalue="" falsevalue="--solid-background" label="Plot on transparent background?" />
8 </when> 8 </when>
9 </xml> 9 </xml>
10 </macros> 10 </macros>
11 <xrefs>
12 <xref type="bio.tools">snipit</xref>
13 </xrefs>
11 <requirements> 14 <requirements>
12 <requirement type="package" version="@TOOL_VERSION@">snipit</requirement> 15 <requirement type="package" version="@TOOL_VERSION@">snipit</requirement>
13 </requirements> 16 </requirements>
17 <version_command>snipit -v</version_command>
14 <command detect_errors="exit_code"><![CDATA[ 18 <command detect_errors="exit_code"><![CDATA[
15 MPLCONFIGDIR=.matplotlib snipit '$alignment' 19 snipit '$alignment'
16 #if str($ref.select) == 'by_id' 20 #if str($ref.select) == 'by_id'
17 -r '$ref.id' 21 -r '$ref.id'
18 #end if 22 #end if
19 #if str($style.labels.choose) 23 #if str($style.labels.choose)
20 -l '$style.labels.source' 24 -l '$style.labels.source'
33 #if $dims.width > 0 37 #if $dims.width > 0
34 --width $dims.width 38 --width $dims.width
35 #end if 39 #end if
36 $dims.size_option 40 $dims.size_option
37 $style.flip_vertical 41 $style.flip_vertical
42 $show_indels
38 #if len($pos_restrict.include_positions) 43 #if len($pos_restrict.include_positions)
39 --include-positions 44 --include-positions
40 #for $p in $pos_restrict.include_positions 45 #for $p in $pos_restrict.include_positions
41 '$p.pos' 46 '$p.pos'
42 #end for 47 #end for
59 --recombi-mode --recombi-references '$style.colouring.parent1,$style.colouring.parent2' 64 --recombi-mode --recombi-references '$style.colouring.parent1,$style.colouring.parent2'
60 #else 65 #else
61 -c $style.colouring.palette 66 -c $style.colouring.palette
62 #end if 67 #end if
63 ]]></command> 68 ]]></command>
69 <environment_variables>
70 <environment_variable name="MPLCONFIGDIR">.matplotlib</environment_variable>
71 </environment_variables>
64 <inputs> 72 <inputs>
65 <param name="alignment" format="fasta" type="data" label="Input alignment fasta file" /> 73 <param name="alignment" format="fasta" type="data" label="Input alignment fasta file" />
66 <conditional name="ref"> 74 <conditional name="ref">
67 <param name="select" type="select" label="The reference sequence ..."> 75 <param name="select" type="select" label="The reference sequence ..."
76 help="Please note that you will HAVE to specify the reference explicitly via its ID if you choose the 'recombinant mutations colouring' scheme and in this case the reference can NOT be one of the recombinant parents.">
68 <option value="first">is the first sequence in the input</option> 77 <option value="first">is the first sequence in the input</option>
69 <option value="by_id">should be picked via its ID</option> 78 <option value="by_id">should be picked via its ID</option>
70 </param> 79 </param>
71 <when value="first" /> 80 <when value="first" />
72 <when value="by_id"> 81 <when value="by_id">
165 <param argument="--size-option" type="select" value="scale" label="Plot sizing options"> 174 <param argument="--size-option" type="select" value="scale" label="Plot sizing options">
166 <option value="--size-option expand">expand</option> 175 <option value="--size-option expand">expand</option>
167 <option value="" selected="true">scale</option> 176 <option value="" selected="true">scale</option>
168 </param> 177 </param>
169 </section> 178 </section>
179 <param argument="--show-indels" type="boolean" truevalue="--show-indels" falsevalue="" label="Try to plot indels" help="This is newly introduced functionality for which you may encounter bugs still." />
170 <param argument="--write-snps" type="boolean" truevalue="-s" falsevalue="" label="Write out SNPs?" help="Produces extra CSV output with lists of SNPs per sequence in the alignment if enabled." /> 180 <param argument="--write-snps" type="boolean" truevalue="-s" falsevalue="" label="Write out SNPs?" help="Produces extra CSV output with lists of SNPs per sequence in the alignment if enabled." />
171 </inputs> 181 </inputs>
172 <outputs> 182 <outputs>
173 <data name="snp_plot" format="png" label="snipit on ${on_string}: Plot" from_work_dir="snp_plot.*"> 183 <data name="snp_plot" format="png" label="snipit on ${on_string}: Plot" from_work_dir="snp_plot.*">
174 <change_format> 184 <change_format>
277 </assert_contents> 287 </assert_contents>
278 </output> 288 </output>
279 </test> 289 </test>
280 <test expect_num_outputs="1"> 290 <test expect_num_outputs="1">
281 <param name="alignment" value="input.fasta" /> 291 <param name="alignment" value="input.fasta" />
292 <conditional name="ref">
293 <param name="select" value="by_id" />
294 <param name="id" value="reference" />
295 </conditional>
282 <section name="style"> 296 <section name="style">
283 <conditional name="colouring"> 297 <conditional name="colouring">
284 <param name="palette" value="" /> 298 <param name="palette" value="" />
285 <param name="parent1" value="USA_1" /> 299 <param name="parent1" value="USA_1" />
286 <param name="parent2" value="USA_5" /> 300 <param name="parent2" value="USA_5" />