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comparison rnacode.xml @ 2:434332033e82 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
author rnateam
date Fri, 13 Apr 2018 07:40:08 -0400
parents 7a84c6c1c4e0
children d49b9759e294
comparison
equal deleted inserted replaced
1:7a84c6c1c4e0 2:434332033e82
1 <tool id="rbc_rnacode" name="RNAcode" version="0.3.0"> 1 <tool id="rbc_rnacode" name="RNAcode" version="0.3.1">
2 <description>Analyze the protein coding potential in MSA.</description> 2 <description>Analyze the protein coding potential in MSA.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.3">rnacode</requirement> 4 <requirement type="package" version="0.3">rnacode</requirement>
5 </requirements> 5 </requirements>
6 <stdio>
7 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
8 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
9 </stdio>
10 <version_command>RNAcode --version</version_command> 6 <version_command>RNAcode --version</version_command>
11 <command> 7 <command detect_errors="exit_code">
12 <![CDATA[ 8 <![CDATA[
13 RNAcode 9 #if $cond_breakmaf.select_breakmaf == 'breakmaf'
14 10 '$__tool_directory__/breakMAF.pl'
11 --maxlength $cond_breakmaf.maxlength
12 --desiredLength $cond_breakmaf.desiredlength
13 < '$alignment' |
14 #else
15 cat '$alignment' |
16 #end if
17
18 #if $cond_breakmaf.select_breakmaf == 'breakmaf' and $cond_breakmaf.processseparately == 'yes'
19 '$__tool_directory__/processMAF.sh'
20 #else
21 RNAcode
22 #end if
23
15 $outputFormat 24 $outputFormat
16 25
17 #if $cutoff and $cutoff is not None 26 #if $cutoff and $cutoff is not None
18 --cutoff $cutoff 27 --cutoff $cutoff
19 #end if 28 #end if
26 $best_region 35 $best_region
27 $best_only 36 $best_only
28 37
29 #if $cond_generateEPS.generateEPS == 'create' 38 #if $cond_generateEPS.generateEPS == 'create'
30 --eps 39 --eps
40 --eps-dir eps/
31 #if $cond_generateEPS.eps_cutoff and $cond_generateEPS.eps_cutoff is not None 41 #if $cond_generateEPS.eps_cutoff and $cond_generateEPS.eps_cutoff is not None
32 --eps-cutoff $cond_generateEPS.eps_cutoff 42 --eps-cutoff $cond_generateEPS.eps_cutoff
33 #end if 43 #end if
34 #end if 44 #end if
35 45
36 #if $cond_scoringParameters.scoringParameters == 'custom' 46 #if $cond_scoringParameters.scoringParameters == 'custom'
37 --pars "$pars" 47 --pars "$pars"
38 #end if 48 #end if
39
40 $alignment
41 49
42 #if $outputFormat.value == '--tabular' 50 #if $outputFormat.value == '--tabular'
43 --outfile $outFileDefault 51 --outfile $outFileDefault
44 #elif $outputFormat.value == '--gtf' 52 #elif $outputFormat.value == '--gtf'
45 --outfile $outFileGTF 53 --outfile $outFileGTF
47 55
48 ]]> 56 ]]>
49 </command> 57 </command>
50 <inputs> 58 <inputs>
51 <param name="alignment" type="data" format="clustal,maf" label="Multiple Alignment" help="Alignment needs to be formatted in ClustalW or MAF format"/> 59 <param name="alignment" type="data" format="clustal,maf" label="Multiple Alignment" help="Alignment needs to be formatted in ClustalW or MAF format"/>
60 <conditional name="cond_breakmaf">
61 <param name="select_breakmaf" type="select" label="Break long alignment blocks" help="If your alignments contain blocks of long genomic regions it is usually not reasonable to score these long regions as a whole.">
62 <option value="keepmaf" selected="true">Process original alignment</option>
63 <option value="breakmaf">Break long alignment blocks</option>
64 </param>
65 <when value="breakmaf">
66 <param argument="--maxLength" name="maxlength" type="integer" optional="true" value="400" label="maxLength" help="Break all blocks longer than that."/>
67 <param argument="--desiredLength" name="desiredlength" type="integer" optional="true" value="200" label="desiredLength" help="Try to create blocks of this size."/>
68 <param name="processseparately" type="boolean" value="false" truevalue="yes" falsevalue="no" label="process blocks separately" help="If enables RNAcode is called separately for each block. This might be a reasonable strategy if RNAcode fails for some blocks."/>
69 </when>
70 <when value="keepmaf"/>
71 </conditional>
52 <param argument="--cutoff" name="cutoff" type="float" optional="true" value="1.0" label="Cutoff" help="Show only regions that have a p-value below the given number. By default all hits are shown."/> 72 <param argument="--cutoff" name="cutoff" type="float" optional="true" value="1.0" label="Cutoff" help="Show only regions that have a p-value below the given number. By default all hits are shown."/>
53 <param argument="--num_samples" name="num_samples" type="integer" optional="true" value="100" label="Number of samples" help="Number of random alignments that are sampled to calculate the p-value. RNAcode estimates the significance of a coding prediction by sampling a given number of random alignments. Default is 100 which gives reasonably stable p-values that are useful for assessing the relevance of a prediction."/> 73 <param argument="--num_samples" name="num_samples" type="integer" optional="true" value="100" label="Number of samples" help="Number of random alignments that are sampled to calculate the p-value. RNAcode estimates the significance of a coding prediction by sampling a given number of random alignments. Default is 100 which gives reasonably stable p-values that are useful for assessing the relevance of a prediction."/>
54 <param argument="--stop_early" name="stop_early" type="boolean" truevalue="--stop-early" falsevalue="" checked="false" label="Stop early" help="Setting this option stops the sampling process as soon as it is clear that the best hit will not fall below the given p-value cutoff. For example, assume a p-value cutoff of 0.05 (see --cutoff) and a sample size of 1000 is given (see --num-samples). As soon as 50 random samples score better than the original alignment, the process is stopped and all hits in the original alignment are reported as p>0.05 (or by convention as 1.0 in gtf and tabular output)."/> 74 <param argument="--stop_early" name="stop_early" type="boolean" truevalue="--stop-early" falsevalue="" checked="false" label="Stop early" help="Setting this option stops the sampling process as soon as it is clear that the best hit will not fall below the given p-value cutoff. For example, assume a p-value cutoff of 0.05 (see --cutoff) and a sample size of 1000 is given (see --num-samples). As soon as 50 random samples score better than the original alignment, the process is stopped and all hits in the original alignment are reported as p>0.05 (or by convention as 1.0 in gtf and tabular output)."/>
55 <param argument="--best_region" name="best_region" type="boolean" truevalue="--best-region" falsevalue="" checked="false" label="Show only best non-overlapping hits" help="By default all positive scoring segments are shown in the output if they fall below the given p-value cutoff. If two hits overlap (different frame or different strand) and --best_region is given only the hit with the highest score is shown. Strong coding regions often lead to statistically significant signals also in other frames. These hits are suppressed by this option and only the correct reading frame is reported."/> 75 <param argument="--best_region" name="best_region" type="boolean" truevalue="--best-region" falsevalue="" checked="false" label="Show only best non-overlapping hits" help="By default all positive scoring segments are shown in the output if they fall below the given p-value cutoff. If two hits overlap (different frame or different strand) and --best_region is given only the hit with the highest score is shown. Strong coding regions often lead to statistically significant signals also in other frames. These hits are suppressed by this option and only the correct reading frame is reported."/>
56 <param argument="--best_only" name="best_only" type="boolean" truevalue="--best-only" falsevalue="" checked="false" label="Show only best hit" help="This options shows only the one single best hit for each alignment."/> 76 <param argument="--best_only" name="best_only" type="boolean" truevalue="--best-only" falsevalue="" checked="false" label="Show only best hit" help="This options shows only the one single best hit for each alignment."/>
87 <data name="outFileGTF" format="gtf" label="${tool.name} on ${on_string}"> 107 <data name="outFileGTF" format="gtf" label="${tool.name} on ${on_string}">
88 <filter>outputFormat == '--gtf'</filter> 108 <filter>outputFormat == '--gtf'</filter>
89 </data> 109 </data>
90 <collection name="output_eps" type="list" label="Plots for ${tool.name} on ${on_string}"> 110 <collection name="output_eps" type="list" label="Plots for ${tool.name} on ${on_string}">
91 <filter>cond_generateEPS['generateEPS'] == "create"</filter> 111 <filter>cond_generateEPS['generateEPS'] == "create"</filter>
92 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.eps" directory="eps" ext="eps" visible="false"/> 112 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.eps" directory="eps" ext="eps"/>
93 </collection> 113 </collection>
94 </outputs> 114 </outputs>
95 <tests> 115 <tests>
96 <test> 116 <test>
97 <param name="alignment" value="coding.aln"/> 117 <param name="alignment" value="coding.aln"/>
99 <param name="outputFormat" value="--tabular"/> 119 <param name="outputFormat" value="--tabular"/>
100 <output name="outFileDefault" ftype="tabular" file="rnacode_result1.tabular" compare="sim_size"/> 120 <output name="outFileDefault" ftype="tabular" file="rnacode_result1.tabular" compare="sim_size"/>
101 <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented --> 121 <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented -->
102 </test> 122 </test>
103 <test> 123 <test>
124 <param name="alignment" value="coding.aln"/>
125 <param name="generateEPS" value="nocreate"/>
126 <param name="outputFormat" value="--tabular"/>
127 <output name="outFileDefault" ftype="tabular" file="rnacode_result1.tabular" compare="sim_size"/>
128 <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented -->
129 </test>
130 <test>
104 <param name="alignment" value="coding.maf"/> 131 <param name="alignment" value="coding.maf"/>
132 <conditional name="cond_breakmaf">
133 <param name="select_breakmaf" value="breakmaf"/>
134 </conditional>
135 <param name="generateEPS" value="nocreate"/>
136 <param name="outputFormat" value="--gtf"/>
137 <output name="outFileGTF" ftype="gtf" file="rnacode_result2.gtf" compare="sim_size"/>
138 <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented -->
139 </test>
140 <test>
141 <param name="alignment" value="coding.maf"/>
142 <conditional name="cond_breakmaf">
143 <param name="select_breakmaf" value="breakmaf"/>
144 <param name="processseparately" value="yes"/>
145 </conditional>
105 <param name="generateEPS" value="nocreate"/> 146 <param name="generateEPS" value="nocreate"/>
106 <param name="outputFormat" value="--gtf"/> 147 <param name="outputFormat" value="--gtf"/>
107 <output name="outFileGTF" ftype="gtf" file="rnacode_result2.gtf" compare="sim_size"/> 148 <output name="outFileGTF" ftype="gtf" file="rnacode_result2.gtf" compare="sim_size"/>
108 <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented --> 149 <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented -->
109 </test> 150 </test>