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comparison recentrifuge.xml @ 1:fe733f05c2f8 draft

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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
author iuc
date Fri, 26 Aug 2022 10:57:30 +0000
parents 09b7b0b2e2c2
children b5407cc2bf51
comparison
equal deleted inserted replaced
0:09b7b0b2e2c2 1:fe733f05c2f8
5 Robust comparative analysis and contamination removal for metagenomics 5 Robust comparative analysis and contamination removal for metagenomics
6 </description> 6 </description>
7 <macros> 7 <macros>
8 <import>macro.xml</import> 8 <import>macro.xml</import>
9 </macros> 9 </macros>
10 <expand macro='edam'/>
10 <expand macro='xrefs'/> 11 <expand macro='xrefs'/>
11 <expand macro="requirements" /> 12 <expand macro="requirements" />
12 <expand macro="version_command" /> 13 <expand macro="version_command" />
13 <command detect_errors="aggressive"><![CDATA[ 14 <command detect_errors="aggressive"><![CDATA[
15 #import re
16 #*======================================
17 Make a dir with all input files
18 ======================================*#
19 mkdir input_dir &&
20 #for $input in $input_file
21 #set input_identifier = re.sub('[^\s\w\-]', '_', str($input.element_identifier))
22 #if $file_type.filetype == "centrifuge"
23 ln -s '$input' 'input_dir/${input_identifier}.out' &&
24 #else if $file_type.filetype == "clark"
25 ln -s '$input' 'input_dir/${input_identifier}.csv' &&
26 #else if $file_type.filetype == "kraken"
27 ln -s '$input' 'input_dir/${input_identifier}.krk' &&
28 #else
29 ln -s '$input' 'input_dir/$input_identifier' &&
30 #end if
31 #end for
14 #*====================================== 32 #*======================================
15 database input 33 database input
16 ======================================*# 34 ======================================*#
17 rcf 35 rcf
18 -n $database.database_name.fields.path 36 -n $database.database_name.fields.path
19 #*====================================== 37 #*======================================
20 Recentrifuge input file 38 Recentrifuge input file
21 ======================================*# 39 ======================================*#
40
22 #if $file_type.filetype == "centrifuge" 41 #if $file_type.filetype == "centrifuge"
23 -f '$input_file' 42 -f input_dir
43 #set $default_scoring = 'SHEL'
44 #else if $file_type.filetype == "kraken"
45 -k input_dir
46 #set $default_scoring = 'KRAKEN'
47 #else if $file_type.filetype == "clark"
48 -r input_dir
24 #set $default_scoring = 'SHEL' 49 #set $default_scoring = 'SHEL'
25 #else if $file_type.filetype == "lmat" 50 #else if $file_type.filetype == "lmat"
26 -l '$input_file' 51 -l input_dir
27 #set $default_scoring = 'LMAT' 52 #set $default_scoring = 'LMAT'
28 #else if $file_type.filetype == "clark"
29 -r '$input_file'
30 #set $default_scoring = 'SHEL'
31 #else if $file_type.filetype == "kraken"
32 -k '$input_file'
33 #set $default_scoring = 'KRAKEN'
34 #else if $file_type.filetype == "generic" 53 #else if $file_type.filetype == "generic"
35 -g '$input_file' 54 -g input_dir
36 --format '$file_type.format' 55 --format '$file_type.format'
37 #set $default_scoring = 'GENERIC' 56 #set $default_scoring = 'GENERIC'
38 #end if 57 #end if
58
39 #*====================================== 59 #*======================================
40 Output options 60 Output options
41 ======================================*# 61 ======================================*#
42 -e $output_option.extra 62 -e $output_option.extra
43 -o output 63 -o output
81 $more_advanced_option.strain 101 $more_advanced_option.strain
82 $more_advanced_option.sequential 102 $more_advanced_option.sequential
83 #*====================================== 103 #*======================================
84 Log file output 104 Log file output
85 ======================================*# 105 ======================================*#
86 &> $logfile 106 | tee "$logfile"
87 ]]> 107 ]]>
88 </command> 108 </command>
89 <inputs> 109 <inputs>
90 <!-- INPUT FILES --> 110 <!-- INPUT FILES -->
91 <param name="input_file" type="data" format="tabular" label="Select taxonomy file tabular formated"/> 111 <param name="input_file" type="data" format="tabular" multiple="true" optional="false" label="Select taxonomy file tabular formated"/>
92 <conditional name="file_type"> 112 <conditional name="file_type">
93 <param name="filetype" type="select" display="radio" label="Type of input file (Centrifuge, CLARK, Generic, Kraken, LMAT)" help="(-f, -r, -g, -k, -l)"> 113 <param name="filetype" type="select" display="radio" label="Type of input file (Centrifuge, CLARK, Generic, Kraken, LMAT)" help="(-f, -r, -g, -k, -l)">
94 <option value="centrifuge">Centrifuge</option> 114 <option value="centrifuge">Centrifuge</option>
95 <option value="clark">CLARK</option> 115 <option value="clark">CLARK</option>
96 <option value="generic">Generic</option> 116 <option value="generic">Generic</option>
124 <option value="DYNOMICS">DYNOMICS</option> 144 <option value="DYNOMICS">DYNOMICS</option>
125 <option value="FULL">FULL</option> 145 <option value="FULL">FULL</option>
126 <option value="TSV" >TSV</option> 146 <option value="TSV" >TSV</option>
127 </param> 147 </param>
128 <param argument="--nohtml" type="boolean" truevalue="--nohtml" falsevalue="" label="Suppress saving the HTML output file" help="remove html output"/> 148 <param argument="--nohtml" type="boolean" truevalue="--nohtml" falsevalue="" label="Suppress saving the HTML output file" help="remove html output"/>
149 <param name="no_logfile" type="boolean" truevalue="True" falsevalue="False" label="Remove the log file"/>
129 </section> 150 </section>
130 <!-- ADVANCED OPTIONS --> 151 <!-- ADVANCED OPTIONS -->
131 <section name="advanced_option" title="Coarse tuning of algorithm parameters"> 152 <section name="advanced_option" title="Coarse tuning of algorithm parameters">
132 <param name="controls" type="integer" optional="true" value="0" label="Number of first samples will be treated as negative controls" help="Add control samples (default is 0)"/> 153 <param name="controls" type="integer" optional="true" value="0" label="Number of first samples will be treated as negative controls" help="Add control samples (default is 0)"/>
133 <param name="scoring" type="select" optional="true" label="Type of scoring to be applied" help="Scoring algorithm, depending of the input files, see the help section of the tools"> 154 <param name="scoring" type="select" optional="true" label="Type of scoring to be applied" help="Scoring algorithm, depending of the input files, see the help section of the tools">
182 <!-- OUTPUT FILE, TYPE DEPENDING ON extra PARAMETER --> 203 <!-- OUTPUT FILE, TYPE DEPENDING ON extra PARAMETER -->
183 <outputs> 204 <outputs>
184 <data name="html_report" format="html" from_work_dir="output.rcf.html" label="${tool.name} on ${on_string}: html report"> 205 <data name="html_report" format="html" from_work_dir="output.rcf.html" label="${tool.name} on ${on_string}: html report">
185 <filter> output_option['nohtml'] == False</filter> 206 <filter> output_option['nohtml'] == False</filter>
186 </data> 207 </data>
187 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file"/> 208 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file">
209 <filter> output_option['no_logfile'] == False </filter>
210 </data>
188 <data name="data_csv" format="tabular" from_work_dir="output.rcf.data.csv" label="${tool.name} on ${on_string}: data.csv"> 211 <data name="data_csv" format="tabular" from_work_dir="output.rcf.data.csv" label="${tool.name} on ${on_string}: data.csv">
189 <filter> output_option['extra'] == 'CSV' </filter> 212 <filter> output_option['extra'] == 'CSV' </filter>
190 </data> 213 </data>
191 <data name="stat_csv" format="tabular" from_work_dir="output.rcf.stat.csv" label="${tool.name} on ${on_string}: stat.csv"> 214 <data name="stat_csv" format="tabular" from_work_dir="output.rcf.stat.csv" label="${tool.name} on ${on_string}: stat.csv">
192 <filter> output_option['extra'] == 'CSV' </filter> 215 <filter> output_option['extra'] == 'CSV' </filter>
267 <param name="strain" value="true"/> 290 <param name="strain" value="true"/>
268 </section> 291 </section>
269 <output name="data_tsv" file="kraken_test/test3_rcf.data.tsv" lines_diff="2"/> 292 <output name="data_tsv" file="kraken_test/test3_rcf.data.tsv" lines_diff="2"/>
270 <output name="stat_tsv" file="kraken_test/test3_rcf.stat.tsv" lines_diff="2"/> 293 <output name="stat_tsv" file="kraken_test/test3_rcf.stat.tsv" lines_diff="2"/>
271 <output name="logfile" file="kraken_test/test3_tsv.log" lines_diff="12"/> 294 <output name="logfile" file="kraken_test/test3_tsv.log" lines_diff="12"/>
295 </test>
296 <test expect_num_outputs="3"> <!-- Test sumarized output TEST_4 -->
297 <section name="database">
298 <param name="database_name" value="test-db-2022"/>
299 </section>
300 <param name="input_file" value="centrifuge_test/centrifuge.out,centrifuge_test/centrifuge_1.out,centrifuge_test/centrifuge_2.out"/>
301 <conditional name="file_type">
302 <param name="filetype" value="centrifuge"/>
303 </conditional>
304 <section name="output_option" >
305 <param name="extra" value="TSV"/>
306 <param name="no_logfile" value="True"/>
307 </section>
308 <section name="advanced_option">
309 <param name="scoring" value="LENGTH"/>
310 </section>
311 <section name="more_advanced_option">
312 <param name="summary" value="ADD"/>
313 <param name="strain" value="true"/>
314 </section>
315 <output name="data_tsv" file="centrifuge_test/test4_rcf.data.tsv" lines_diff="2"/>
316 <output name="stat_tsv" file="centrifuge_test/test4_rcf.stat.tsv" lines_diff="2"/>
317 <output name="html_report" file="centrifuge_test/test4_tsv.html" lines_diff="12"/>
272 </test> 318 </test>
273 </tests> 319 </tests>
274 <help><![CDATA[ 320 <help><![CDATA[
275 **What it does** 321 **What it does**
276 322