isoformswitchanalyzer: isoformswitchanalyzer.xml annotate

annotate isoformswitchanalyzer.xml @ 7:d3377a16d881 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878

author	iuc
date	Wed, 14 Jan 2026 09:30:42 +0000
parents	b3f292d9f35d
children

rev	line source
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1 <tool id="isoformswitchanalyzer" name="IsoformSwitchAnalyzeR" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	2 <description>statistical identification of isoform switching</description>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	3 <macros>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	4 <import>macros.xml</import>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	5 </macros>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	6 <expand macro='xrefs'/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	7 <expand macro='requirements'/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	8 <stdio>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	9 <regex match="Execution halted"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	10 source="both"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	11 level="fatal"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	12 description="Execution halted." />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	13 <regex match="Error in"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	14 source="both"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	15 level="fatal"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	16 description="An undefined error occurred, please check your input carefully and contact your administrator." />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	17 <regex match="Fatal error"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	18 source="both"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	19 level="fatal"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	20 description="An undefined error occurred, please check your input carefully and contact your administrator." />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	21 </stdio>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	22 <command><![CDATA[
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	23 #set $conditions = list()
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	24 #set $sampleIDs = list()
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	25 #set $replicates = list()
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	26 #if $functionMode.selector == 'data_import'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	27 #if $functionMode.transcriptome.is_of_type("fasta.gz"):
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	28 ln -s '${functionMode.transcriptome}' './transcriptome.fasta.gz' &&
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	29 #set $transcriptome = './transcriptome.fasta.gz'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	30 #else
1 2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf iuc parents: 0 diff changeset	31 ln -s '${functionMode.transcriptome}' './transcriptome.fasta' &&
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	32 #set $transcriptome = './transcriptome.fasta'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	33 #end if
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	34 #if $functionMode.genomeAnnotation.is_of_type("gtf.gz"):
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	35 ln -s '${functionMode.genomeAnnotation}' './annotation.gtf.gz' &&
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	36 #set $annotation = './annotation.gtf.gz'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	37 #else
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	38 ln -s '${functionMode.genomeAnnotation}' './annotation.gtf' &&
1 2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf iuc parents: 0 diff changeset	39 #set $annotation = './annotation.gtf'
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	40 #end if
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	41 mkdir -p 'input_files' &&
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	42 #if $functionMode.countFiles != 'disabled':
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	43 mkdir -p "count_files/factor1/" &&
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	44 mkdir -p "count_files/factor2/" &&
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	45 #end if
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	46 #if $functionMode.tool_source.selector == 'stringtie'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	47 #set $filename = 't_data.ctab'
2 2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	48 #if $functionMode.tool_source.novoisoforms.selector == 'novel'
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	49 #if $functionMode.tool_source.novoisoforms.stringtieAnnotation.is_of_type("gtf.gz"):
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	50 ln -s '${$functionMode.tool_source.novoisoforms.stringtieAnnotation}' './stringtie_annotation.gtf.gz' &&
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	51 #set $stringtie_annotation = './stringtie_annotation.gtf.gz'
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	52 #else
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	53 ln -s '${$functionMode.tool_source.novoisoforms.stringtieAnnotation}' './stringtie_annotation.gtf' &&
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	54 #set $stringtie_annotation = './stringtie_annotation.gtf'
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	55 #end if
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	56 #end if
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	57 #else if $functionMode.tool_source.selector == 'salmon'
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	58 #set $filename = 'quant.sf'
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	59 #else
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	60 #set $filename = 'abundance.tsv'
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	61 #end if
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	62
7 d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	63 ## read cofactor repeats and generate cofactor_map dictionary
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	64 ## cofactor_map structure: {file_path: {cofactor_name: cofactor_level_name, ...}, ...}
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	65 #set $cofactor_map = {}
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	66 #set $cofactor_names = []
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	67 #for $cofactor_item in $functionMode.tool_source.cofactor:
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	68 #set $cofactor_name = str($cofactor_item.cofactor_name)
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	69 $cofactor_names.append($cofactor_name)
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	70 #for $level_item in $cofactor_item.cofactor_level:
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	71 #set $level_name = str($level_item.cofactor_level_name)
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	72 #for $level_file in $level_item.cofactor_level_files:
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	73 #set $file_path = str($level_file)
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	74 #if $file_path not in $cofactor_map:
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	75 #set $cofactor_map[$file_path] = {}
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	76 #end if
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	77 #set $cofactor_map[$file_path][$cofactor_name] = $level_name
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	78 #end for
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	79 #end for
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	80 #end for
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	81
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	82 ## create file_to_sample_map dictionary
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	83 #set $file_to_sample_map = {}
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	84
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	85 #for $index in range(len($functionMode.tool_source.first_factor.trans_counts)):
7 d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	86 #set $sampleID = str($functionMode.tool_source.first_factor.factorLevel) + str($index)
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	87 #set $trans_file = $functionMode.tool_source.first_factor.trans_counts[$index]
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	88 #set $file_to_sample_map[$sampleID] = str($trans_file)
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	89 $conditions.append($functionMode.tool_source.first_factor.factorLevel)
7 d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	90 $sampleIDs.append($sampleID)
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	91 $replicates.append($index)
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	92 mkdir './input_files/${functionMode.tool_source.first_factor.factorLevel}${index}/' &&
7 d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	93 ln -s $trans_file './input_files/${functionMode.tool_source.first_factor.factorLevel}${index}/${filename}' &&
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	94 #end for
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	95
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	96 #for $index in range(len($functionMode.tool_source.second_factor.trans_counts)):
7 d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	97 #set $sampleID = str($functionMode.tool_source.second_factor.factorLevel) + str($index)
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	98 #set $trans_file = $functionMode.tool_source.second_factor.trans_counts[$index]
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	99 #set $file_to_sample_map[$sampleID] = str($trans_file)
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	100 $conditions.append($functionMode.tool_source.second_factor.factorLevel)
7 d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	101 $sampleIDs.append($sampleID)
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	102 $replicates.append($index)
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	103 mkdir './input_files/${functionMode.tool_source.second_factor.factorLevel}${index}/' &&
7 d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	104 ln -s $trans_file './input_files/${functionMode.tool_source.second_factor.factorLevel}${index}/${filename}' &&
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	105 #end for
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	106
7 d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	107
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	108 Rscript '${__tool_directory__}/IsoformSwitchAnalyzeR.R'
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	109 #for $i, $condition in enumerate($conditions)
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	110 --condition $condition
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	111 --sampleID $sampleIDs[$i]
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	112 --replicate $replicates[$i]
7 d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	113 #set $sample_file = $file_to_sample_map[$sampleIDs[$i]]
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	114 #if $sample_file in $cofactor_map
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	115 #set $cofactor_values = []
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	116 #for $cofactor_name in $cofactor_names:
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	117 #if $cofactor_name in $cofactor_map[$sample_file]
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	118 #set $cofactor_value = $cofactor_map[$sample_file][$cofactor_name]
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	119 #silent $cofactor_values.append(str($cofactor_value))
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	120 #end if
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	121 #end for
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	122 --cofactors $(','.join($cofactor_values))
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	123 #end if
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	124 #end for
7 d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	125 #if len($cofactor_names) > 0
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	126 --cofactorNames $(','.join($cofactor_names))
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	127 #end if
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	128 $functionMode.pairedSamples
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	129 --modeSelector $functionMode.selector
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	130 --parentDir './input_files'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	131 --annotation $annotation
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	132 --transcriptome $transcriptome
2 2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	133 $functionMode.removeNonConvensionalChr
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	134 --toolSource $functionMode.tool_source.selector
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	135 #if $functionMode.tool_source.selector == 'stringtie'
2 2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	136 #if $functionMode.tool_source.novoisoforms.selector == 'novel'
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	137 --stringtieAnnotation $stringtie_annotation
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	138 #end if
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	139 --readLength $functionMode.tool_source.averageSize
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	140 $functionMode.tool_source.fixStringTieAnnotationProblem
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	141 #end if
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	142 --countFiles $functionMode.countFiles
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	143 #else if $functionMode.selector == 'first_step'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	144 Rscript '${__tool_directory__}/IsoformSwitchAnalyzeR.R'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	145 --modeSelector $functionMode.selector
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	146 --rObject $functionMode.robject
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	147 --alpha $functionMode.alpha
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	148 --dIFcutoff $functionMode.dIFcutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	149 $functionMode.onlySigIsoforms
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	150 $functionMode.filterForConsequences
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	151 --geneExpressionCutoff $functionMode.prefilter.geneExpressionCutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	152 --isoformExpressionCutoff $functionMode.prefilter.isoformExpressionCutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	153 --IFcutoff $functionMode.prefilter.IFcutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	154 $functionMode.prefilter.removeSingleIsformGenes
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	155 $functionMode.prefilter.keepIsoformInAllConditions
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	156 $functionMode.dexseq.correctForConfoundingFactors
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	157 $functionMode.dexseq.overwriteIFvalues
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	158 $functionMode.dexseq.reduceToSwitchingGenes
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	159 $functionMode.dexseq.reduceFurtherToGenesWithConsequencePotential
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	160 $functionMode.dexseq.keepIsoformInAllConditions
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	161 --minORFlength $functionMode.novel_isoform.minORFlength
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	162 --orfMethod $functionMode.novel_isoform.orfMethod
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	163 --PTCDistance $functionMode.novel_isoform.PTCDistance
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	164 $functionMode.extract_sequence.removeShortAAseq
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	165 $functionMode.extract_sequence.removeLongAAseq
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	166 $functionMode.extract_sequence.removeORFwithStop
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	167 $functionMode.extract_sequence.onlySwitchingGenes
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	168 #else
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	169 #if $functionMode.protein_domains.selector == 'enabled'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	170 mkdir -p './pfam_files' &&
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	171 #for $index,$filename in enumerate($functionMode.protein_domains.analyzePFAM)
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	172 ln -s $filename './pfam_files/dataset${index}.txt' &&
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	173 #end for
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	174 #end if
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	175 #if $functionMode.signal_peptides.selector == 'enabled'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	176 mkdir -p './signalp_files' &&
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	177 #for $index,$filename in enumerate($functionMode.signal_peptides.analyzeSignalP)
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	178 ln -s $filename './signalp_files/dataset${index}.txt' &&
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	179 #end for
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	180 #end if
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	181 #if $functionMode.disordered_regions.selector == 'netsurfp'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	182 mkdir -p './netsurf_files' &&
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	183 #for $index,$filename in enumerate($functionMode.disordered_regions.analyzeNetSurfP2)
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	184 ln -s $filename './netsurf_files/dataset${index}.txt' &&
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	185 #end for
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	186 #end if
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	187 Rscript '${__tool_directory__}/IsoformSwitchAnalyzeR.R'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	188 --modeSelector $functionMode.selector
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	189 --rObject $functionMode.robject
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	190 --analysisMode $functionMode.analysis_mode.selector
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	191 --alpha $functionMode.analysis_mode.alpha
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	192 --dIFcutoff $functionMode.analysis_mode.dIFcutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	193 #if $functionMode.analysis_mode.selector == 'top'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	194 --genesToPlot $functionMode.analysis_mode.n
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	195 $functionMode.analysis_mode.advanced_options.filterForConsequences
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	196 $functionMode.analysis_mode.advanced_options.sortByQvals
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	197 $functionMode.analysis_mode.advanced_options.onlySigIsoforms
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	198 $functionMode.analysis_mode.advanced_options.onlySwitchingGenes
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	199 $functionMode.analysis_mode.advanced_options.countGenes
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	200 $functionMode.analysis_mode.advanced_options.asFractionTotal
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	201 $functionMode.analysis_mode.advanced_options.plotGenes
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	202 $functionMode.analysis_mode.advanced_options.simplifyLocation
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	203 $functionMode.analysis_mode.advanced_options.removeEmptyConsequences
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	204 $functionMode.analysis_mode.advanced_options.removeEmptyConsequences
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	205 #else
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	206 --gene $functionMode.analysis_mode.gene
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	207 --IFcutoff $functionMode.analysis_mode.advanced_options.IFcutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	208 $functionMode.analysis_mode.advanced_options.rescaleTranscripts
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	209 $functionMode.analysis_mode.advanced_options.reverseMinus
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	210 $functionMode.analysis_mode.advanced_options.addErrorbars
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	211 $functionMode.analysis_mode.advanced_options.onlySwitchingGenes
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	212 #end if
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	213 #if $functionMode.coding_potential.selector == 'cpat'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	214 --pathToCPATresultFile $functionMode.coding_potential.analyzeCPAT
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	215 --codingCutoff $functionMode.coding_potential.codingCutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	216 #else if $functionMode.coding_potential.selector == 'cpc2'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	217 --pathToCPC2resultFile $functionMode.coding_potential.analyzeCPC2
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	218 $functionMode.coding_potential.removeNoncodingORFs
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	219 --codingCutoff $functionMode.coding_potential.codingCutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	220 #end if
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	221 #if $functionMode.protein_domains.selector == 'enabled'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	222 --pathToPFAMresultFile './pfam_files'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	223 #end if
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	224 #if $functionMode.signal_peptides.selector == 'enabled'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	225 --pathToSignalPresultFile './signalp_files'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	226 --minSignalPeptideProbability $functionMode.signal_peptides.minSignalPeptideProbability
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	227 #end if
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	228 #if $functionMode.disordered_regions.selector == 'netsurfp'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	229 --pathToNetSurfP2resultFile './netsurf_files'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	230 --smoothingWindowSize $functionMode.disordered_regions.smoothingWindowSize
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	231 --probabilityCutoff $functionMode.disordered_regions.probabilityCutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	232 --minIdrSize $functionMode.disordered_regions.minIdrSize
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	233 #else if $functionMode.disordered_regions.selector == 'iupred2a'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	234 --pathToIUPred2AresultFile $functionMode.disordered_regions.AanalyzeIUPred2A
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	235 --smoothingWindowSize $functionMode.disordered_regions.smoothingWindowSize
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	236 --probabilityCutoff $functionMode.disordered_regions.probabilityCutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	237 --minIdrSize $functionMode.disordered_regions.minIdrSize
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	238 $functionMode.disordered_regions.annotateBindingSites
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	239 --minIdrBindingSize $functionMode.disordered_regions.minIdrBindingSize
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	240 --minIdrBindingOverlapFrac $functionMode.disordered_regions.minIdrBindingOverlapFrac
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	241 #end if
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	242 --ntCutoff $functionMode.analyzeSwitchConsequences.ntCutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	243 #if $functionMode.analyzeSwitchConsequences.ntFracCutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	244 --ntFracCutoff $functionMode.analyzeSwitchConsequences.ntFracCutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	245 #end if
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	246 --ntJCsimCutoff $functionMode.analyzeSwitchConsequences.ntJCsimCutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	247 --AaCutoff $functionMode.analyzeSwitchConsequences.AaCutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	248 --AaFracCutoff $functionMode.analyzeSwitchConsequences.AaFracCutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	249 --AaJCsimCutoff $functionMode.analyzeSwitchConsequences.AaJCsimCutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	250 $functionMode.analyzeSwitchConsequences.removeNonConseqSwitches
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	251 #if $functionMode.analysis_mode.selector == 'top'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	252 && mkdir -p './pdf_outputs/'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	253 && mv *pdf './pdf_outputs/'
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	254 && mv _vs_ gene_plots
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	255 #end if
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	256 #end if
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	257 ]]></command>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	258 <inputs>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	259 <conditional name="functionMode">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	260 <param name="selector" type="select" label="Tool function mode"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	261 help="The first step of a IsoformSwitchAnalyzeR workflow is to import and integrate the isoform quantification
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	262 with its basic annotation. Once you have all the relevant data imported into R (IsoformSwitchAnalyzeR will
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	263 also help you with that), the workflow for identification and analysis of isoform switches with functional
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	264 consequences can be divided into two parts.">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	265 <option value="data_import">Import data</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	266 <option value="first_step">Analysis part one: Extract isoform switches and their sequences</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	267 <option value="second_step">Analysis part two: Plot all isoform switches and their annotation</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	268 </param>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	269 <when value="data_import">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	270 <conditional name="tool_source">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	271 <param name="selector" type="select" label="Quantification data source" help="IsoformSwitchAnalyzeR has different functions for importing data from different sources.">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	272 <option value="stringtie">StringTie</option>
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	273 <option value="salmon">Salmon</option>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	274 <option value="kallisto">Kallisto</option>
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	275 </param>
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	276 <when value="salmon">
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	277 <expand macro="macro_inputs"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	278 </when>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	279 <when value="kallisto">
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	280 <expand macro="macro_inputs"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	281 </when>
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	282 <when value="stringtie">
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	283 <expand macro="macro_inputs"/>
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	284 <param name="averageSize" type="integer" min="0" value="150" label="Average read length" help="Must be the number of base pairs sequenced. e.g. if the data
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	285 quantified is 75 bp paired ends the the user should supply readLength=75" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	286 <param argument="fixStringTieAnnotationProblem" type="boolean" truevalue="--fixStringTieAnnotationProblem" falsevalue="" checked="true"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	287 label="Fix StringTie annotation problem" help="This option will automatically try and correct some of the annoation problems created when
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	288 doing transcript assembly (unassigned transcripts and merged genes)" />
2 2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	289 <conditional name="novoisoforms">
4 512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	290 <param name="selector" type="select" label="Analysis mode">
2 2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	291 <option value="novel">Include novel isoforms in analysis</option>
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	292 <option value="reference">Reference-only analysis</option>
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	293 </param>
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	294 <when value="novel">
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	295 <param name="stringtieAnnotation" type="data" format="gtf,gtf.gz" label="Annotation generated by StringTie merge"
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	296 help="The merged GTF is used to recalculate expression estimates using the merged, novel transcripts." />
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	297 </when>
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	298 <when value="reference"/>
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	299 </conditional>
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	300 </when>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	301 </conditional>
2 2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	302 <param name="genomeAnnotation" type="data" format="gtf,gtf.gz" label="Genome annotation"
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	303 help="It is used to integrate the coding sequence (CDS) regions from in the GTF file as the ORF regions used by IsoformSwitchAnalyzeR." />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	304 <param name="transcriptome" type="data" format="fasta,fasta.gz" label="Transcriptome"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	305 help="Please note this different from a fasta file with the sequences of the entire genome." />
2 2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	306 <param argument="removeNonConvensionalChr" type="boolean" truevalue="--removeNonConvensionalChr" falsevalue="" checked="false"
2b0a6af4b85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit d00628bfc2ac36914885e0941a2b4453ca0bff9a iuc parents: 1 diff changeset	307 label="Remove non-conventional chromosomes" help="These regions are typically used to annotate regions that cannot be associated to a specific region." />
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	308 <param argument="pairedSamples" type="boolean" truevalue="--pairedSamples" falsevalue="" checked="false" label="Paired samples between factors" help="Samples
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	309 from different factors belong to the same individual (e.g. samples from same patient from health and cancerous tissues or different parts from the same plant)" />
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	310 <param name="countFiles" type="select" label="Generate count matrix files" help="If IsoformSwitchAnalyzeR is used for fixing Stringtie annotation
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	311 problem, it can generate count files for analyzing differential expression with DESeq2 (when selecting collection) or CEMiTool (when secting the expression matrix format).">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	312 <option value="disabled">Disabled</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	313 <option value="collection">Collection of count files</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	314 <option value="matrix">Expression matrix</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	315 </param>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	316 </when>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	317
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	318 <!--WRAPPER FIRST STEP SECTION-->
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	319
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	320 <when value="first_step">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	321 <param name="robject" type="data" format="rdata" label="IsoformSwitchAnalyzeR R object" help="It is generated when running the analysis part 1." />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	322 <expand macro="macro_alpha_difcutoff"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	323 <expand macro="macro_onlysigisoforms1"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	324 <param argument="filterForConsequences" type="boolean" truevalue="--filterForConsequences" falsevalue="" checked="false"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	325 label="Filter for consquences" help="Filter for genes with functional consequences. The output will then be the number of significant genes
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	326 and isoforms originating from genes with predicted consequences" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	327 <section name="prefilter" title="Pre-filter parameters" help="SwitchAnalyzeR will remove genes/isoforms with the aim of allowing faster
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	328 processing time as well as more trustworthy results.">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	329 <param argument="geneExpressionCutoff" type="float" min="0" value="1" label="Gene expression cutoff" help="The expression cutoff (most
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	330 likely in TPM/RPKM/FPKM) which the average expression in BOTH condisions must be higher than." />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	331 <param argument="isoformExpressionCutoff" type="float" min="0" value="0" label="Isoform expresion cutoff" help="The expression cutoff (most
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	332 likely in RPKM/FPKM) which isoforms must be expressed more than, in at least one conditions of a comparison. Default is 0 (which removes
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	333 completely unused isoforms)." />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	334 <expand macro="macro_ifcutoff" value="0.01" help="The cutoff on isoform usage (measured as Isoform Fraction) which isoforms must be used more
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	335 than in at least one conditions of a comparison" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	336 <param argument="removeSingleIsformGenes" type="boolean" truevalue="--removeSingleIsformGenes" falsevalue="" checked="true" label="Remove single isoform genes"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	337 help="Only keep genes containing more than one isoform (in any comparison, after the other filters have been applied)" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	338 <expand macro="macro_keeisoforminall" checked="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	339 </section>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	340 <section name="dexseq" title="DEXseq parameters" help="DEXSeq is used to test isoforms (isoform resolution) for differential isoform usage.">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	341 <param argument="correctForConfoundingFactors" type="boolean" truevalue="--correctForConfoundingFactors" falsevalue="" checked="true" label="Correct for confounding factors"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	342 help="A logic indicating whether IsoformSwitchAnalyzeR to use limma to correct for any confounding effects (e.g. batch effects) as indicated in the
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	343 design matrix (as additional columns (apart from the two default columns)) " />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	344 <param argument="overwriteIFvalues" type="boolean" truevalue="--overwriteIFvalues" falsevalue="" checked="true" label="Overwrite IF values" help="It indicates
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	345 whether to overwrite the IF and dIF stored in the switchAnalyzeRlist with the corrected IF and dIF values - if no confounding effects are
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	346 present in the design matrix this will not change anything" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	347 <param argument="reduceToSwitchingGenes" type="boolean" truevalue="--reduceToSwitchingGenes" falsevalue="" checked="true" label="Reduce to switch genes" help="Reduced to the
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	348 genes which contains at least one isoform significantly differential used (as indicated by the alpha and dIFcutoff parameters" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	349 <param argument="reduceFurtherToGenesWithConsequencePotential" type="boolean" truevalue="--reduceFurtherToGenesWithConsequencePotential" falsevalue="" checked="false"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	350 label="Reduce to genes with consequence potential" help="This argument is a more strict version of reduceToSwitchingGenes
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	351 as it not only requires that at least one isoform is significantly differential used (as indicated by the alpha and dIFcutoff parameters) but also that there is an isoform
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	352 with the opposite effect size (e.g. used less if the first isoform is used more). The minimum effect size of the opposing isoform usage is also controlled by dIFcutoff.
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	353 The existence of such an opposing isoform means a switch pair can be formed" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	354 <expand macro="macro_keeisoforminall" checked="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	355 </section>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	356 <section name="novel_isoform" title="Novel isoform analysis parameters" help="For the subset of isoforms not already annotated with ORFs this
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	357 function predicts the most likely Open Reading Frame (ORF) and the NMD sensitivity. This function is made to help annotate
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	358 isoforms if you have performed (guided) de-novo isoform reconstruction (isoform deconvolution).">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	359 <param argument="minORFlength" type="integer" min="0" value="100" label="Minimum ORF length" help="The minimum size (in nucleotides) an
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	360 ORF must be to be considered (and reported). Default is 100 nucleotides, which around 97.5% of Gencode coding isoforms in both human and mouse have." />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	361 <param argument="orfMethod" type="select" label="ORF identification method" help="More information in the help section">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	362 <option value="longest.AnnotatedWhenPossible">Longest and annotated when possible</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	363 <option value="longest">Longest</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	364 <option value="mostUpstream">Most upstream</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	365 <option value="longestAnnotated">Longest annotated</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	366 <option value="mostUpstreamAnnoated">Most upstream annotated</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	367 </param>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	368 <param argument="PTCDistance" type="integer" min="0" value="50" label="Maximal allowed premature termination codon-distance" help="The minimum
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	369 distance (number of nucleotides) from the STOP codon to the final exon-exon junction. If the distance from the STOP to the final exon-exon
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	370 junction is larger than this the isoform to be marked as NMD-sensitive. " />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	371 </section>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	372 <section name="extract_sequence" title="Sequence extraction parameters" help="switchAnalyzeR will extracts the nucleotide (NT) sequence of transcripts by
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	373 extracting and concatenating the sequences of a reference genome corresponding to the genomic coordinates of the isoforms. ">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	374 <expand macro="macro_onlyswitching"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	375 <param argument="removeShortAAseq" type="boolean" truevalue="--removeShortAAseq" falsevalue="" checked="true" label="Remove short aminoacid sequences" help="This
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	376 option exist to allows for easier usage of the Pfam and SignalP web servers which both currently have restrictions on allowed sequence lengths. If
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	377 enabled AA sequences are filtered to be > 5 AA. This will only affect the sequences written to the FASTA file not the sequences added to the switchAnalyzeRlist" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	378 <param argument="removeLongAAseq" type="boolean" truevalue="--removeLongAAseq" falsevalue="" checked="false" label="Remove long aminoacid sequences" help="A
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	379 logical indicating whether to removesequences based on their length. This option exist to allows for easier usage of the Pfam and SignalP web servers
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	380 which both currently have restrictions on allowed sequence lengths. If enabled AA sequences are filtered to be smaller 1000 AA. This will only affect the
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	381 sequences written to the fasta file (if writeToFile=TRUE) not the sequences added to the switchAnalyzeRlist. " />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	382 <param argument="removeORFwithStop" type="boolean" truevalue="--removeORFwithStop" falsevalue="" checked="true" label="Remove ORFs containint STOP codons" help="ORFs
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	383 containing stop codons, defined as * when the ORF nucleotide sequences is translated to the amino acid sequence, should be A) removed from the ORF
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	384 annotation in the switchAnalyzeRlist and B) removed from the sequences added to the switchAnalyzeRlist and/or written to FASTA files. This is only
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	385 necessary if you are analyzing quantified known annotated data where you supplied a GTF file to the import function" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	386 </section>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	387 <param name="outputs_first" type="select" display="checkboxes" multiple="true" label="Outputs selector">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	388 <option value="nt" selected="true">Nucleotide sequences</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	389 <option value="aa" selected="true">Aminoacid sequences</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	390 <option value="summary" selected="true">Gene switch summary</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	391 </param>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	392 </when>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	393
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	394 <!-- WRAPPER SECOND STEP SECTION-->
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	395
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	396 <when value="second_step">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	397 <param name="robject" type="data" format="rdata" label="IsoformSwitchAnalyzeR R object" help="It is generated when running the analysis part 2." />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	398 <conditional name="analysis_mode">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	399 <param name="selector" type="select" label="Analysis mode" help="This selector allows so specify if you want to analyze a specific gene or
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	400 the (top) switching genes/isoforms ">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	401 <option value="top" selected="true">Full analysis</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	402 <option value="single">Analyze specific gene</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	403 </param>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	404 <when value="top">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	405 <expand macro="macro_alpha_difcutoff"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	406 <param argument="n" type="integer" min="1" value="10" label="Number of top switching features (genes/isoforms) to plot"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	407 help="This parameters allows to specify the number of top genes/isoforms to plot"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	408 <section name="advanced_options" title="Full analysis advanced options">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	409 <param argument="filterForConsequences" type="boolean" truevalue="--filterForConsequences" falsevalue="" checked="false" label="Filter genes with functional consequences"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	410 help="The output will then be the number of significant genes and isoforms originating from genes with predicted consequences"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	411 <param argument="sortByQvals" type="boolean" truevalue="--sortByQvals" falsevalue="" checked="true" label="Sorting mode" help="A logic indicating
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	412 whether to the top n features are sorted by decreasing significance (increasing q-values) (if enabled) or decreasing switch size
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	413 (absolute dIF, which are still significant as defined by alpha) (if disabled). The dIF values for genes are considered as the total
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	414 change within the gene calculated as sum(abs(dIF)) for each gene" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	415 <expand macro="macro_onlysigisoforms2"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	416 <expand macro="macro_onlyswitching"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	417 <param argument="countGenes" type="boolean" truevalue="--countGenes" falsevalue="" checked="true" label="Number genes or isoform switches counts" help="This parameter indicates
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	418 whether it is the number of genes (if enabled) or isoform switches (if disabled) which primary result in gain/loss that are counted" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	419 <param argument="asFractionTotal" type="boolean" truevalue="--asFractionTotal" falsevalue="" checked="false" label="Summary as numbers of as fraction" help="The consequences/splicing events
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	420 should be summarized calculated as numbers (if disabled) or as a fraction of the total number of switches/genes" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	421 <param argument="plotGenes" type="boolean" truevalue="--plotGenes" falsevalue="" checked="false" label="Plot number/fraction of genes or isoforms" help="Plot the number/fraction of genes with
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	422 (if enabled) or isoforms (if disabled) involved with isoform switches with functional consequences (both filtered via alpha and dIFcutoff)" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	423 <param argument="simplifyLocation" type="boolean" truevalue="--simplifyLocation" falsevalue="" checked="true" label="Simplify location" help="Simplify the switches involved in changes
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	424 in subcellular localizations (due the the hundreds of possible combinations)" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	425 <param argument="removeEmptyConsequences" type="boolean" truevalue="--removeEmptyConsequences" falsevalue="" checked="false" label="Remove empty consequences" help="Remove consequenses analyzed
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	426 but where no differences was found (those showing zero in the plot)" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	427 <param argument="analysisOppositeConsequence" type="boolean" truevalue="--analysisOppositeConsequence" falsevalue="" checked="false"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	428 label="Analysis opposite consequences in enrichment analysis" help="Reverse the analysis meaning if 'Domain gains' are analyze will case the analysis to be performed on 'Domain loss'.
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	429 The main effect is for the visual appearance of plot which will be mirrored (around the 0.5 fraction)" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	430 </section>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	431 </when>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	432 <when value="single">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	433 <param argument="gene" type="text" value="" label="Gene name" help="Either the gene_id or the gene name of the gene to plot">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	434 <sanitizer invalid_char="">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	435 <valid initial="string.letters,string.digits">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	436 <add value="_" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	437 <add value="-" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	438 </valid>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	439 </sanitizer>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	440 <validator type="regex">[0-9a-zA-Z_-]+</validator>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	441 </param>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	442 <expand macro="macro_alpha_difcutoff"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	443 <section name="advanced_options" title="Single gene mode advanced options">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	444 <expand macro="macro_ifcutoff" value="0.05" help="The cutoff used for the minimum contribution to gene expression (in at least one
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	445 condition) for an isoforms must have to be plotted (measured as Isoform Fraction (IF) values)" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	446 <param argument="rescaleTranscripts" type="boolean" truevalue="--rescaleTranscripts" falsevalue="" checked="true" label="Rescale transcripts"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	447 help="All the isoforms should be resealed to the square root of their original sizes. This feature is implemented because
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	448 introns usually are much larger than exons making it difficult to see structural changes. This is very useful for structural
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	449 visualization but the scaling might distort actual intron and exon sizes" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	450 <param argument="reverseMinus" type="boolean" truevalue="--reverseMinus" falsevalue="" checked="true" label="Isoforms on minus strand
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	451 should be inverted" help="Isoforms on minus strand should be inverted so they are visualized as going from left to right
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	452 instead of right to left" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	453 <param argument="addErrorbars" type="boolean" truevalue="--addErrorbars" falsevalue="" checked="true" label="Add error bars" help="Error
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	454 bars should be added to the expression plots to show uncertainty in estimates" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	455 <expand macro="macro_onlyswitching"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	456 </section>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	457 </when>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	458 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	459 <conditional name="coding_potential">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	460 <param name="selector" type="select" label="Include prediction of coding potential information"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	461 help="Integrate in the analysis de output from CPAT or CPC2.">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	462 <option value="disabled">Disabled</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	463 <option value="cpat">CPAT</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	464 <option value="cpc2">CPC2</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	465 </param>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	466 <when value="disabled"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	467 <when value="cpat">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	468 <param argument="analyzeCPAT" type="data" format="txt" label="CPAT result file"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	469 help=" Use default parameters and the nucleotide fasta file (_nt.fasta). If the webserver was used, download the tab-delimited
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	470 result file (available at the bottom of the result page). If a stand-alone version was used, just supply the path to the result file" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	471 <param argument="codingCutoff" type="float" min="0" max="1" value="0.725" label="Coding cutoff" help="cutoff used by CPAT for distinguishing between
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	472 coding and non-coding transcripts. The cutoff is dependent on species analyzed. IsoformSwitchAnalyzerR developers suggest that the optimal cutoff
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	473 for overlapping coding and noncoding isoforms are 0.725 for human and 0.721 for mouse. However the suggested cutoffs from the CPAT develpers
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	474 derived by comparing known genes to random non-coding regions of the genome is 0.364 for human and 0.44 for mouse" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	475 </when>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	476 <when value="cpc2">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	477 <param argument="analyzeCPC2" type="data" format="txt" label="CPC2 result file"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	478 help="Use default parameters and if required select the most similar species. If the webserver (batch submission) was used,
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	479 download the tab-delimited result file (via the “Download the result” button). If a stand-alone version was just just supply the path to the result file" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	480 <param argument="removeNoncodingORFs" type="boolean" truevalue="--removeNoncodingORFs" falsevalue="" checked="false" label="Remove non-coding ORFs" help="Remove ORF information
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	481 from the isoforms which the CPC2 analysis classifies as non-coding. This can be particular useful if the isoform (and ORF) was predicted de-novo but is not
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	482 recommended if ORFs was imported from a GTF file" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	483 <param argument="codingCutoff" type="float" min="0" max="1" value="0.5" label="Coding cutoff" help="Numeric indicating the cutoff used by CPC2 for distinguishing
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	484 between coding and non-coding transcripts. The cutoff appears to be species independent." />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	485 </when>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	486 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	487 <conditional name="protein_domains">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	488 <param name="selector" type="select" label="Include Pfam information" help="Pfam is a database of protein families that includes their annotations and multiple sequence
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	489 alignments generated using hidden Markov models.">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	490 <option value="disabled">Disabled</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	491 <option value="enabled">Enabled</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	492 </param>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	493 <when value="disabled"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	494 <when value="enabled">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	495 <param argument="analyzePFAM" type="data" format="txt" multiple="true" optional="true" label="Include Pfam results (sequence analysis of protein domains)" help="Use default
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	496 parameters and the amino acid fasta file (_AA.fasta). If the webserver is used you need to copy/paste the result part of the mail you receive into an empty plain text
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	497 document (notepad, sublimetext, TextEdit or similar (not Word)) and save that to a plain text (txt) file. The path to that file should be supplied. If a stand-alone
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	498 version was used, just supply the path to the result file" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	499 </when>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	500 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	501 <conditional name="signal_peptides">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	502 <param name="selector" type="select" label="Include SignalP results" help="Integration of the result of SignalP (external sequence analysis of signal peptides)">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	503 <option value="disabled">Disabled</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	504 <option value="enabled">Enabled</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	505 </param>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	506 <when value="disabled"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	507 <when value="enabled">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	508 <param argument="analyzeSignalP" type="data" format="txt" multiple="true" optional="true" label="SignalP" help="Use the amino acid fasta file (_AA.fasta). If using the webserver SignalP
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	509 should be run with the parameter 'Short output (no figures)' under 'Output format' and one should select the appropriate 'Organism group'. When
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	510 using a stand-alone version SignalP should be run with the '-f summary' option. If using the webserver the results can be downloaded using the
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	511 'Downloads' button in the top-right corner where the user should select 'Prediction summary' and supply the path to the resulting file to the
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	512 'pathToSignalPresultFile' argument. If a stand-alone version was just supply the path to the summary result file." />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	513 <param argument="minSignalPeptideProbability" type="float" min="0" max="1" value="0.5" label="Minimum probability for calling a signal peptide"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	514 </when>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	515 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	516
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	517 <conditional name="disordered_regions">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	518 <param name="selector" type="select" label="Include prediction of intrinsically disordered Regions (IDR) information"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	519 help="Integrate in the analysis de output from IUPred2A or NetSurfP-2">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	520 <option value="disabled">Disabled</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	521 <option value="iupred2a">IUPred2A</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	522 <option value="netsurfp">NetSurfP-2</option>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	523 </param>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	524 <when value="disabled"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	525 <when value="iupred2a">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	526 <param argument="AanalyzeIUPred2A" type="data" format="txt,gz" label="IUPred2A result file" help="Can be gziped. If
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	527 multiple result files were created (multiple web-server runs) just supply all of them." />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	528 <expand macro="macro_disordered_regions"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	529 <param argument="annotateBindingSites" type="boolean" truevalue="--annotateBindingSites" falsevalue="" checked="true" label="Annotate binding sites"
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	530 help="Integrate the ANCHOR2 prediction of Intrinsically Disordered Binding Regions (IDBRs)" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	531 <param argument="minIdrBindingSize" type="integer" min="0" value="15" label="Minimum IDBR binding size" help="How long a stretch of
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	532 binding site the region part of the Intrinsically Disordered Binding Regions (IDBR)" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	533 <param argument="minIdrBindingOverlapFrac" type="float" min="0" value="0.8" label="Minimum fraction of a predicted IDBR" help="Minimum
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	534 fraction of a predicted IDBR must also be within a IDR before the IDR is considered as a an IDR with a binding region" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	535 </when>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	536 <when value="netsurfp">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	537 <param argument="analyzeNetSurfP2" type="data" format="txt,gz" multiple="true" label="NetSurfP-2 result file" help="Can be gziped. If
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	538 multiple result files were created (multiple web-server runs) just supply all of them." />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	539 <expand macro="macro_disordered_regions"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	540 </when>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	541 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	542 <section name="analyzeSwitchConsequences" title="Analyze switch consequences parameters">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	543 <param argument="ntCutoff" type="integer" min="0" value="50" label="Nucleotide length cutoff" help="The length difference (in nucleotides) a
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	544 comparison must be larger than for reporting differences" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	545 <param argument="ntFracCutoff" type="float" min="0" max="1" optional="true" label="Nucleotide length fraction cutoff" help="The cutoff in length
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	546 difference, measured as a fraction of the length of the downregulated isoform, a comparison must be larger than for
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	547 reporting differences. For example does 0.05 mean the upregulated isoform must be 5% longer/shorter before it is reported. " />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	548 <param argument="ntJCsimCutoff" type="float" min="0" max="1" value="0.8" label="Cutoff on Jaccard similarity between the overlap of two nucloetide sequences" help=" If the
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	549 measured JCsim is smaller than this cutoff the sequences are considered different and reported as such" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	550 <param argument="AaCutoff" type="integer" min="0" value="10" label="Aminoacid lenght cutoff" help="Length difference (in AA) a comparison must be larger
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	551 than for reporting differences when evaluating ’ORF_seq_similarity’, primarily implemented to avoid differences in very short AA sequences being
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	552 classified as different" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	553 <param argument="AaFracCutoff" type="float" min="0" max="1" value="0.5" label="Aminoacid length fraction cutoff" help="Cutoff of length difference of
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	554 the protein domain or IDR. The difference is measured as a fraction of the longest region, a comparison must be larger than before reporting it" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	555 <param argument="AaJCsimCutoff" type="float" min="0" max="1" value="0.9" label="Cutoff between the overlap of two aminoacid sequences" help="If the
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	556 measured JCsim is smaller than this cutoff the sequences are considered different and reported as such" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	557 <param argument="removeNonConseqSwitches" type="boolean" truevalue="--removeNonConseqSwitches" falsevalue="" checked="true" label="Remove the comparison of isoforms
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	558 where no consequences were found" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	559 </section>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	560 </when>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	561 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	562 </inputs>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	563 <outputs>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	564 <collection name="collection_counts_factor1" type="list" label="${tool.name} on ${on_string}: gene counts factor1">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	565 <discover_datasets pattern="__designation_and_ext__" format="tabular" directory="count_files/factor1" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	566 <filter>functionMode['selector'] == 'data_import'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	567 <filter>functionMode['countFiles'] == 'collection'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	568 </collection>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	569 <collection name="collection_counts_factor2" type="list" label="${tool.name} on ${on_string}: gene counts factor2">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	570 <discover_datasets pattern="__designation_and_ext__" format="tabular" directory="count_files/factor2" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	571 <filter>functionMode['selector'] == 'data_import'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	572 <filter>functionMode['countFiles'] == 'collection'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	573 </collection>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	574 <data name="matrix_counts" format="tabular" from_work_dir="count_files/matrix.tabular" label="${tool.name} on ${on_string}: gene counts matrix">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	575 <filter>functionMode['selector'] == 'data_import'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	576 <filter>functionMode['countFiles'] == 'matrix'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	577 </data>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	578 <data name="sample_annotation" format="tabular" from_work_dir="count_files/samples.tabular" label="${tool.name} on ${on_string}: samples annotation">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	579 <filter>functionMode['selector'] == 'data_import'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	580 <filter>functionMode['countFiles'] == 'matrix'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	581 </data>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	582 <data name="switchList" format="rdata" from_work_dir="SwitchList.Rda" label="${tool.name} on ${on_string}: SwitchList (RData)"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	583 <data name="isoformAA" format="fasta" from_work_dir="isoformSwitchAnalyzeR_isoform_AA.fasta" label="${tool.name} on ${on_string}: aminoacid sequences">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	584 <filter>functionMode['selector'] == 'first_step'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	585 <filter>functionMode['outputs_first'] and 'aa' in functionMode['outputs_first']</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	586 </data>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	587 <data name="isoformNT" format="fasta" from_work_dir="isoformSwitchAnalyzeR_isoform_nt.fasta" label="${tool.name} on ${on_string}: nucleotide sequences">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	588 <filter>functionMode['selector'] == 'first_step'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	589 <filter>functionMode['outputs_first'] and 'nt' in functionMode['outputs_first']</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	590 </data>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	591 <data name="switchSummary" format="tabular" from_work_dir="switchSummary.tsv" label="${tool.name} on ${on_string}: summary">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	592 <filter>functionMode['selector'] == 'first_step'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	593 <filter>functionMode['outputs_first'] and 'summary' in functionMode['outputs_first']</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	594 </data>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	595 <collection name="plots_summary" type="list" label="${tool.name} on ${on_string}: genome wide plots">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	596 <discover_datasets pattern="__designation_and_ext__" format="pdf" directory="pdf_outputs" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	597 <filter>functionMode['selector'] == 'second_step'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	598 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	599 </collection>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	600 <collection name="genes_consequences" type="list" label="${tool.name} on ${on_string}: isoform switches with predicted functional consequences plots">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	601 <discover_datasets pattern="__designation_and_ext__" format="pdf" directory="gene_plots/with_consequences" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	602 <filter>functionMode['selector'] == 'second_step'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	603 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	604 </collection>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	605 <collection name="genes_wo_consequences" type="list" label="${tool.name} on ${on_string}: isoform switches without predicted functional consequences plots">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	606 <discover_datasets pattern="__designation_and_ext__" format="pdf" directory="gene_plots/without_consequences" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	607 <filter>functionMode['selector'] == 'second_step'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	608 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	609 </collection>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	610 <data name="mostSwitching" format="tabular" from_work_dir="mostSwitchingGene.tsv" label="${tool.name} on ${on_string}: switching gene/isoforms">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	611 <filter>functionMode['selector'] == 'second_step'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	612 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	613 </data>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	614 <data name="consequencesSummary" format="tabular" from_work_dir="consequencesSummary.tsv" label="${tool.name} on ${on_string}: consequences summary">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	615 <filter>functionMode['selector'] == 'second_step'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	616 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	617 </data>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	618 <data name="consequencesEnrichment" format="tabular" from_work_dir="consequencesEnrichment.tsv" label="${tool.name} on ${on_string}: consequences enrichment">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	619 <filter>functionMode['selector'] == 'second_step'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	620 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	621 </data>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	622 <data name="splicingSummary" format="tabular" from_work_dir="splicingSummary.tsv" label="${tool.name} on ${on_string}: splicing summary">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	623 <filter>functionMode['selector'] == 'second_step'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	624 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	625 </data>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	626 <data name="splicingEnrichment" format="tabular" from_work_dir="splicingEnrichment.tsv" label="${tool.name} on ${on_string}: splicing enrichment">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	627 <filter>functionMode['selector'] == 'second_step'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	628 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	629 </data>
4 512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	630 <data name="splicing_fulldata" format="tabular" from_work_dir="switchSplicing_fulldata.tsv" label="${tool.name} on ${on_string}: alternative splicing full data">
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	631 <filter>functionMode['selector'] == 'second_step'</filter>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	632 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	633 </data>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	634 <data name="consequences_fulldata" format="tabular" from_work_dir="switchConsequence_fulldata.tsv" label="${tool.name} on ${on_string}: funcional consequences full data">
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	635 <filter>functionMode['selector'] == 'second_step'</filter>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	636 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	637 </data>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	638 <data name="isoformFeatures" format="tabular" from_work_dir="IsoformFeatures.tsv" label="${tool.name} on ${on_string}: isoform features">
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	639 <filter>functionMode['selector'] == 'second_step'</filter>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	640 <filter>functionMode['analysis_mode']['selector'] == 'top'</filter>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	641 </data>
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	642 <data name="single_gene" format="pdf" from_work_dir="single_gene.pdf" label="${tool.name} on ${on_string}: single gene analysis">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	643 <filter>functionMode['selector'] == 'second_step'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	644 <filter>functionMode['analysis_mode']['selector'] == 'single'</filter>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	645 </data>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	646 </outputs>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	647 <tests>
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	648 <!-- Test 01: Data import mode-->
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	649 <test expect_num_outputs="1">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	650 <conditional name="functionMode">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	651 <param name="selector" value="data_import"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	652 <param name="genomeAnnotation" value="annotation_salmon.gtf.gz"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	653 <param name="transcriptome" value="transcriptome.fasta.gz"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	654 <param name="countFiles" value="disabled"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	655 <conditional name="tool_source">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	656 <param name="selector" value="salmon"/>
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	657 <section name="first_factor">
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	658 <param name="factorLevel" value="health"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	659 <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	660 </section>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	661 <section name="second_factor">
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	662 <param name="factorLevel" value="cancer"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	663 <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	664 </section>
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	665 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	666 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	667 <output name="switchList" file="test01.RData" ftype="rdata" compare="sim_size" delta="100"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	668 </test>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	669 <!-- Test 02: Data import mode generate expression matrix-->
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	670 <test expect_num_outputs="3">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	671 <conditional name="functionMode">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	672 <param name="selector" value="data_import"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	673 <param name="genomeAnnotation" value="annotation_salmon.gtf.gz"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	674 <param name="transcriptome" value="transcriptome.fasta.gz"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	675 <param name="countFiles" value="matrix"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	676 <conditional name="tool_source">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	677 <param name="selector" value="salmon"/>
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	678 <section name="first_factor">
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	679 <param name="factorLevel" value="health"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	680 <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	681 </section>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	682 <section name="second_factor">
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	683 <param name="factorLevel" value="cancer"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	684 <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	685 </section>
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	686 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	687 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	688 <output name="switchList" ftype="rdata">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	689 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	690 <has_size value="652170" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	691 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	692 </output>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	693 <output name="matrix_counts" file="test02_counts.tabular" ftype="tabular" lines_diff="6"/>
7 d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	694 <output name="sample_annotation">
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	695 <assert_contents>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	696 <has_text_matching expression="sampleID\s+condition"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	697 <has_text_matching expression="health0\s+health"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	698 <has_text_matching expression="health1\s+health"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	699 <has_text_matching expression="cancer0\s+cancer"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	700 <has_text_matching expression="cancer1\s+cancer"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	701 </assert_contents>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	702 </output>
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	703 </test>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	704 <!-- Test 03: Data import mode generate collection count files-->
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	705 <test expect_num_outputs="3">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	706 <conditional name="functionMode">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	707 <param name="selector" value="data_import"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	708 <param name="genomeAnnotation" value="annotation_salmon.gtf.gz"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	709 <param name="transcriptome" value="transcriptome.fasta.gz"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	710 <param name="countFiles" value="collection"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	711 <conditional name="tool_source">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	712 <param name="selector" value="salmon"/>
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	713 <section name="first_factor">
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	714 <param name="factorLevel" value="health"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	715 <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	716 </section>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	717 <section name="second_factor">
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	718 <param name="factorLevel" value="cancer"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	719 <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	720 </section>
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	721 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	722 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	723 <output name="switchList" ftype="rdata">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	724 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	725 <has_size value="652170" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	726 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	727 </output>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	728 <output_collection name="collection_counts_factor1" type="list" count="2">
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	729 <element name="health0_dataset" file="test03_health_counts.tabular" ftype="tabular" lines_diff="6"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	730
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	731 </output_collection>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	732 <output_collection name="collection_counts_factor2" type="list" count="2">
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	733 <element name="cancer0_dataset" file="test03_cancer_counts.tabular" ftype="tabular" lines_diff="6"/>
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	734 </output_collection>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	735 </test>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	736 <!-- Test 04: Extract isoform switches all outputs-->
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	737 <test expect_num_outputs="4">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	738 <conditional name="functionMode">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	739 <param name="selector" value="first_step"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	740 <param name="robject" value="test01.RData"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	741 <param name="alpha" value="0.05"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	742 <param name="dIFcutoff" value="0.1"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	743 <param name="onlySigIsoforms" value="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	744 <param name="filterForConsequences" value="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	745 <param name="outputs_first" value="nt,aa,summary"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	746 <section name="prefilter">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	747 <param name="geneExpressionCutoff" value="1"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	748 <param name="isoformExpressionCutoff" value="0"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	749 <param name="IFcutoff" value="0.01"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	750 <param name="removeSingleIsformGenes" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	751 <param name="keepIsoformInAllConditions" value="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	752 </section>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	753 <section name="dexseq">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	754 <param name="correctForConfoundingFactors" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	755 <param name="overwriteIFvalues" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	756 <param name="reduceToSwitchingGenes" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	757 <param name="reduceFurtherToGenesWithConsequencePotential" value="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	758 <param name="keepIsoformInAllConditions" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	759 </section>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	760 <section name="novel_isoform">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	761 <param name="minORFlength" value="100"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	762 <param name="orfMethod" value="longest.AnnotatedWhenPossible"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	763 <param name="PTCDistance" value="50"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	764 </section>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	765 <section name="extract_sequence">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	766 <param name="onlySwitchingGenes" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	767 <param name="removeShortAAseq" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	768 <param name="removeLongAAseq" value="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	769 <param name="removeORFwithStop" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	770 </section>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	771 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	772 <output name="switchList" file="test04.RData" ftype="rdata" compare="sim_size" delta="100"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	773 <output name="isoformAA" ftype="fasta">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	774 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	775 <has_size value="138275" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	776 <has_text text=">TCONS_00000007"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	777 <has_text text="MLLPPGSLSRPRTFSSQPLQT"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	778 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	779 </output>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	780 <output name="isoformNT" ftype="fasta">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	781 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	782 <has_size value="780375" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	783 <has_text text=">TCONS_00000007"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	784 <has_text text="GGGTCTCCCTCTGTTGTCCAAGGC"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	785 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	786 </output>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	787 <output name="switchSummary" file="test04_summary.tabular" ftype="tabular"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	788 </test>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	789 <!-- Test 05: Extract isoform switches alternative parameters-->
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	790 <test expect_num_outputs="1">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	791 <conditional name="functionMode">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	792 <param name="selector" value="first_step"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	793 <param name="robject" value="test01.RData"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	794 <param name="outputs_first" value=""/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	795 <section name="dexseq">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	796 <param name="correctForConfoundingFactors" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	797 <param name="overwriteIFvalues" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	798 <param name="reduceToSwitchingGenes" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	799 <param name="reduceFurtherToGenesWithConsequencePotential" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	800 <param name="keepIsoformInAllConditions" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	801 </section>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	802 <section name="novel_isoform">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	803 <param name="orfMethod" value="mostUpstream"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	804 </section>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	805 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	806 <output name="switchList" ftype="rdata">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	807 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	808 <has_size value="500518" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	809 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	810 </output>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	811 </test>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	812 <!--Test 06: generate plots and summaries full analsys-->
4 512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	813 <test expect_num_outputs="12">
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	814 <conditional name="functionMode">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	815 <param name="selector" value="second_step"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	816 <param name="robject" value="test04.RData"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	817 <section name="analyzeSwitchConsequences">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	818 <param name="ntCutoff" value="50"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	819 <param name="ntJCsimCutoff" value="0.8"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	820 <param name="AaCutoff" value="10"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	821 <param name="AaFracCutoff" value="0.5"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	822 <param name="AaJCsimCutoff" value="0.9"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	823 <param name="removeNonConseqSwitches" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	824 </section>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	825 <conditional name="analysis_mode">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	826 <param name="selector" value="top"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	827 <param name="alpha" value="0.05"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	828 <param name="dIFcutoff" value="0.1"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	829 <param name="n" value="2"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	830 <section name="advanced_options">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	831 <param name="filterForConsequences" value="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	832 <param name="sortByQvals" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	833 <param name="onlySigIsoforms" value="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	834 <param name="onlySwitchingGenes" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	835 <param name="countGenes" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	836 <param name="asFractionTotal" value="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	837 <param name="plotGenes" value="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	838 <param name="simplifyLocation" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	839 <param name="removeEmptyConsequences" value="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	840 <param name="analysisOppositeConsequence" value="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	841 </section>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	842 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	843 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	844 <output name="switchList" ftype="rdata">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	845 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	846 <has_size value="531580" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	847 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	848 </output>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	849 <output_collection name="plots_summary" type="list" count="7">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	850 <element name="consequencesEnrichment" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	851 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	852 <has_size value="5995" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	853 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	854 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	855 <element name="extractConsequencesSummary" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	856 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	857 <has_size value="5681" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	858 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	859 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	860 <element name="splicingEnrichment" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	861 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	862 <has_size value="6361" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	863 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	864 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	865 <element name="splicingGenomewide" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	866 <assert_contents>
1 2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf iuc parents: 0 diff changeset	867 <has_size value="165752" delta="300"/>
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	868 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	869 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	870 <element name="splicingSummary" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	871 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	872 <has_size value="5990" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	873 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	874 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	875 <element name="switchGene" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	876 <assert_contents>
1 2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf iuc parents: 0 diff changeset	877 <has_size value="18432" delta="300"/>
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	878 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	879 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	880 <element name="volcanoPlot" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	881 <assert_contents>
1 2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf iuc parents: 0 diff changeset	882 <has_size value="20147" delta="300"/>
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	883 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	884 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	885 </output_collection>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	886 <output_collection name="genes_consequences" type="list" count="2">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	887 <element name="1_switch_plot_NADK_aka_NADK" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	888 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	889 <has_size value="8716" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	890 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	891 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	892 <element name="2_switch_plot_PRKCZ_aka_PRKCZ" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	893 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	894 <has_size value="8463" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	895 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	896 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	897 </output_collection>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	898 <output_collection name="genes_wo_consequences" type="list" count="2">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	899 <element name="1_switch_plot_CLSTN1_aka_CLSTN1" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	900 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	901 <has_size value="8039" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	902 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	903 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	904 <element name="2_switch_plot_ZBTB40_aka_ZBTB40" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	905 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	906 <has_size value="7506" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	907 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	908 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	909 </output_collection>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	910 <output name="mostSwitching" file="test06_switching.tabular" ftype="tabular" lines_diff="4"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	911 <output name="consequencesSummary" file="test06_consequences_summary.tabular" ftype="tabular" lines_diff="4"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	912 <output name="consequencesEnrichment" file="test06_consequences_enrichment.tabular" ftype="tabular" lines_diff="4"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	913 <output name="splicingSummary" file="test06_splicing_summary.tabular" ftype="tabular" lines_diff="4"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	914 <output name="splicingEnrichment" file="test06_splicing_enrichment.tabular" ftype="tabular" lines_diff="4"/>
4 512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	915 <output name="consequences_fulldata" ftype="tabular">
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	916 <assert_contents>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	917 <has_size value="51508" delta="100"/>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	918 <has_text text="ORF_genomic"/>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	919 </assert_contents>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	920 </output>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	921 <output name="splicing_fulldata" ftype="tabular">
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	922 <assert_contents>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	923 <has_size value="46951" delta="100"/>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	924 <has_text text="ATTS_genomic_start"/>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	925 </assert_contents>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	926 </output>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	927 <output name="isoformFeatures" ftype="tabular">
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	928 <assert_contents>
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	929 <has_size value="94888" delta="100"/>
4 512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	930 <has_text text="gene_overall_mean"/>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	931 </assert_contents>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	932 </output>
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	933 </test>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	934 <!--Test 07: generate plots and summaries full analsys all inputs-->
4 512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	935 <test expect_num_outputs="12">
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	936 <conditional name="functionMode">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	937 <param name="selector" value="second_step"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	938 <param name="robject" value="test04.RData"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	939 <section name="analyzeSwitchConsequences">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	940 <param name="ntCutoff" value="20"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	941 <param name="ntJCsimCutoff" value="0.5"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	942 <param name="AaCutoff" value="10"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	943 <param name="AaFracCutoff" value="0.4"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	944 <param name="AaJCsimCutoff" value="0.8"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	945 <param name="removeNonConseqSwitches" value="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	946 </section>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	947 <conditional name="analysis_mode">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	948 <param name="selector" value="top"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	949 <param name="alpha" value="0.05"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	950 <param name="dIFcutoff" value="0.1"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	951 <param name="n" value="2"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	952 <section name="advanced_options">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	953 <param name="filterForConsequences" value="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	954 <param name="sortByQvals" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	955 <param name="onlySigIsoforms" value="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	956 <param name="onlySwitchingGenes" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	957 <param name="countGenes" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	958 <param name="asFractionTotal" value="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	959 <param name="plotGenes" value="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	960 <param name="simplifyLocation" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	961 <param name="removeEmptyConsequences" value="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	962 <param name="analysisOppositeConsequence" value="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	963 </section>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	964 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	965 <conditional name="coding_potential">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	966 <param name="selector" value="cpc2"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	967 <param name="analyzeCPC2" value="cpc2_result.txt"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	968 <param name="removeNoncodingORFs" value="false"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	969 <param name="codingCutoff" value="0.5"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	970 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	971 <conditional name="protein_domains">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	972 <param name="selector" value="enabled"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	973 <param name="analyzePFAM" value="pfam_results.txt"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	974 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	975 <conditional name="signal_peptides">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	976 <param name="selector" value="enabled"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	977 <param name="analyzeSignalP" value="signalP_results.txt"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	978 <param name="minSignalPeptideProbability" value="0.5"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	979 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	980 <conditional name="disordered_regions">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	981 <param name="selector" value="iupred2a"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	982 <param name="AanalyzeIUPred2A" value="iupred2a_result.txt.gz"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	983 <param name="smoothingWindowSize" value="5"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	984 <param name="probabilityCutoff" value="0.5"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	985 <param name="minIdrSize" value="30"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	986 <param name="annotateBindingSites" value="true"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	987 <param name="minIdrBindingSize" value="15"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	988 <param name="minIdrBindingOverlapFrac" value="0.8"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	989 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	990 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	991 <output name="switchList" ftype="rdata">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	992 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	993 <has_size value="542120" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	994 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	995 </output>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	996 <output_collection name="plots_summary" type="list" count="7">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	997 <element name="consequencesEnrichment" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	998 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	999 <has_size value="5995" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1000 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1001 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1002 <element name="extractConsequencesSummary" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1003 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1004 <has_size value="6617" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1005 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1006 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1007 <element name="splicingEnrichment" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1008 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1009 <has_size value="6361" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1010 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1011 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1012 <element name="splicingGenomewide" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1013 <assert_contents>
1 2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf iuc parents: 0 diff changeset	1014 <has_size value="165752" delta="300"/>
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1015 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1016 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1017 <element name="splicingSummary" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1018 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1019 <has_size value="5990" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1020 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1021 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1022 <element name="switchGene" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1023 <assert_contents>
1 2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf iuc parents: 0 diff changeset	1024 <has_size value="18432" delta="300"/>
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1025 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1026 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1027 <element name="volcanoPlot" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1028 <assert_contents>
1 2c4e879a81cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf iuc parents: 0 diff changeset	1029 <has_size value="20147" delta="300"/>
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1030 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1031 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1032 </output_collection>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1033 <output_collection name="genes_consequences" type="list" count="2">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1034 <element name="1_switch_plot_NADK_aka_NADK" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1035 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1036 <has_size value="8716" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1037 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1038 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1039 <element name="2_switch_plot_PRKCZ_aka_PRKCZ" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1040 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1041 <has_size value="8463" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1042 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1043 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1044 </output_collection>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1045 <output_collection name="genes_wo_consequences" type="list" count="2">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1046 <element name="1_switch_plot_CLSTN1_aka_CLSTN1" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1047 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1048 <has_size value="8559" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1049 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1050 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1051 <element name="2_switch_plot_ZBTB40_aka_ZBTB40" ftype="pdf">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1052 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1053 <has_size value="8051" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1054 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1055 </element>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1056 </output_collection>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1057 <output name="mostSwitching" ftype="tabular">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1058 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1059 <has_size value="4062" delta="50"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1060 <has_text text="RPL11"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1061 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1062 </output>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1063 <output name="consequencesSummary" ftype="tabular">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1064 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1065 <has_size value="1192" delta="50"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1066 <has_text text="nrGenesWithConsequences"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1067 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1068 </output>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1069 <output name="consequencesEnrichment" ftype="tabular">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1070 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1071 <has_size value="1432" delta="50"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1072 <has_text text="NMD insensitive (paired with NMD sensitive"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1073 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1074 </output>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1075 <output name="splicingSummary" ftype="tabular">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1076 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1077 <has_size value="892" delta="50"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1078 <has_text text="MEE in isoform used less"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1079 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1080 </output>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1081 <output name="splicingEnrichment" ftype="tabular">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1082 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1083 <has_size value="1157" delta="50"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1084 <has_text text="A5 gain (paired with A5 loss)"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1085 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1086 </output>
4 512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	1087 <output name="consequences_fulldata" ftype="tabular">
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	1088 <assert_contents>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	1089 <has_size value="103581" delta="50"/>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	1090 <has_text text="signal_peptide_identified"/>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	1091 </assert_contents>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	1092 </output>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	1093 <output name="splicing_fulldata" ftype="tabular">
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	1094 <assert_contents>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	1095 <has_size value="46951" delta="50"/>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	1096 <has_text text="ATTS_genomic_start"/>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	1097 </assert_contents>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	1098 </output>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	1099 <output name="isoformFeatures" ftype="tabular">
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	1100 <assert_contents>
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1101 <has_size value="99310" delta="50"/>
4 512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	1102 <has_text text="gene_overall_mean"/>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	1103 </assert_contents>
512d6462f2ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit fa9a0a8f71ce6da2cd790474454776a9601968c3 iuc parents: 2 diff changeset	1104 </output>
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1105 </test>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1106 <!-- Test 08: analyze single gene-->
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1107 <test expect_num_outputs="2">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1108 <conditional name="functionMode">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1109 <param name="selector" value="second_step"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1110 <param name="robject" value="test04.RData"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1111 <conditional name="analysis_mode">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1112 <param name="selector" value="single"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1113 <param name="gene" value="NADK"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1114 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1115 </conditional>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1116 <output name="single_gene" ftype="pdf" file="test08_single_gene.pdf" compare="sim_size"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1117 <output name="switchList" ftype="rdata">
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1118 <assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1119 <has_size value="531580" delta="300"/>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1120 </assert_contents>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1121 </output>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1122 </test>
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1123 <!-- Test 09: Kallisto input-->
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1124 <test expect_num_outputs="1">
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1125 <conditional name="functionMode">
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1126 <param name="selector" value="data_import"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1127 <param name="genomeAnnotation" value="annotation_kallisto.gtf.gz"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1128 <param name="transcriptome" value="transcriptome_kallisto.fasta.gz"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1129 <param name="countFiles" value="disabled"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1130 <conditional name="tool_source">
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1131 <param name="selector" value="kallisto"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1132 <section name="first_factor">
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1133 <param name="factorLevel" value="health"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1134 <param name="trans_counts" value="kallisto_cond1_rep1.tsv,kallisto_cond1_rep2.tsv"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1135 </section>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1136 <section name="second_factor">
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1137 <param name="factorLevel" value="cancer"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1138 <param name="trans_counts" value="kallisto_cond2_rep1.tsv,kallisto_cond2_rep2.tsv"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1139 </section>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1140 </conditional>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1141 </conditional>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1142 <output name="switchList" file="test09.RData" ftype="rdata" compare="sim_size" delta="100"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1143 </test>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1144 <!-- Test 10: Test paired samples in the experimental design-->
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1145 <test expect_num_outputs="3">
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1146 <conditional name="functionMode">
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1147 <param name="selector" value="data_import"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1148 <param name="genomeAnnotation" value="annotation_salmon.gtf.gz"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1149 <param name="transcriptome" value="transcriptome.fasta.gz"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1150 <param name="pairedSamples" value="true"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1151 <param name="countFiles" value="matrix"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1152 <conditional name="tool_source">
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1153 <param name="selector" value="salmon"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1154 <section name="first_factor">
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1155 <param name="factorLevel" value="health"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1156 <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1157 </section>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1158 <section name="second_factor">
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1159 <param name="factorLevel" value="cancer"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1160 <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1161 </section>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1162 </conditional>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1163 </conditional>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1164 <output name="switchList" ftype="rdata">
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1165 <assert_contents>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1166 <has_size value="652170" delta="300"/>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1167 </assert_contents>
b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1168 </output>
7 d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1169 <output name="sample_annotation">
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1170 <assert_contents>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1171 <has_text_matching expression="sampleID\s+condition\s+replicate"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1172 <has_text_matching expression="health0\s+health\s+0"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1173 <has_text_matching expression="health1\s+health\s+1"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1174 <has_text_matching expression="cancer0\s+cancer\s+0"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1175 <has_text_matching expression="cancer1\s+cancer\s+1"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1176 </assert_contents>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1177 </output>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1178 </test>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1179 <!-- Test 11: Data import mode add cofactor-->
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1180 <test expect_num_outputs="3">
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1181 <conditional name="functionMode">
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1182 <param name="selector" value="data_import"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1183 <param name="genomeAnnotation" value="gencode.hg19.chr10_1000.gtf.gz"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1184 <param name="transcriptome" value="transcriptome_stringtie.fasta.gz"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1185 <param name="countFiles" value="matrix"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1186 <conditional name="tool_source">
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1187 <param name="selector" value="stringtie"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1188 <conditional name="novoisoforms">
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1189 <param name="selector" value="novel"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1190 <param name="stringtieAnnotation" value="annotation_stringtie.gtf.gz"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1191 </conditional>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1192 <section name="first_factor">
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1193 <param name="factorLevel" value="EWS-FLI1"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1194 <param name="trans_counts" value="ASP14_1.tabular,ASP14_2.tabular,ASP14_3.tabular"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1195 </section>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1196 <section name="second_factor">
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1197 <param name="factorLevel" value="no-EWS-FLI1"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1198 <param name="trans_counts" value="ASP14_doxycycline_1.tabular,ASP14_doxycycline_2.tabular,ASP14_doxycycline_3.tabular"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1199 </section>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1200 <repeat name="cofactor">
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1201 <param name="cofactor_name" value="Batch"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1202 <repeat name="cofactor_level">
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1203 <param name="cofactor_level_name" value="batch1"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1204 <param name="cofactor_level_files" value="ASP14_1.tabular,ASP14_doxycycline_1.tabular"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1205 </repeat>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1206 <repeat name="cofactor_level">
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1207 <param name="cofactor_level_name" value="batch2"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1208 <param name="cofactor_level_files" value="ASP14_2.tabular,ASP14_doxycycline_2.tabular"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1209 </repeat>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1210 <repeat name="cofactor_level">
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1211 <param name="cofactor_level_name" value="batch3"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1212 <param name="cofactor_level_files" value="ASP14_3.tabular,ASP14_doxycycline_3.tabular"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1213 </repeat>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1214 </repeat>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1215 <repeat name="cofactor">
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1216 <param name="cofactor_name" value="Age"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1217 <repeat name="cofactor_level">
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1218 <param name="cofactor_level_name" value="20"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1219 <param name="cofactor_level_files" value="ASP14_1.tabular,ASP14_doxycycline_1.tabular,ASP14_2.tabular"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1220 </repeat>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1221 <repeat name="cofactor_level">
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1222 <param name="cofactor_level_name" value="60"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1223 <param name="cofactor_level_files" value="ASP14_doxycycline_2.tabular,ASP14_3.tabular,ASP14_doxycycline_3.tabular"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1224 </repeat>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1225 </repeat>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1226 </conditional>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1227 </conditional>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1228 <output name="switchList" ftype="rdata">
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1229 <assert_contents>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1230 <has_size value="374542" delta="300"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1231 </assert_contents>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1232 </output>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1233 <output name="matrix_counts" file="stringtie_counts.tabular" ftype="tabular" lines_diff="6"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1234 <output name="sample_annotation">
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1235 <assert_contents>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1236 <has_text_matching expression="sampleID\s+condition\s+Batch\s+Age"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1237 <has_text_matching expression="EWSXFLI10\s+EWSXFLI1\s+batch1\s+20"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1238 <has_text_matching expression="EWSXFLI11\s+EWSXFLI1\s+batch2\s+20"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1239 <has_text_matching expression="EWSXFLI12\s+EWSXFLI1\s+batch3\s+60"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1240 <has_text_matching expression="noXEWSXFLI10\s+noXEWSXFLI1\s+batch1\s+20"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1241 <has_text_matching expression="noXEWSXFLI11\s+noXEWSXFLI1\s+batch2\s+60"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1242 <has_text_matching expression="noXEWSXFLI12\s+noXEWSXFLI1\s+batch3\s+60"/>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1243 </assert_contents>
d3377a16d881 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer commit db7d80651213272678725ba877d95f5113378878 iuc parents: 5 diff changeset	1244 </output>
5 b3f292d9f35d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 iuc parents: 4 diff changeset	1245 </test>
0 f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1246 </tests>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1247 <help><![CDATA[
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1248
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1249 .. class:: infomark
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1250
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1251 Purpose
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1252
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1253 IsoformSwitchAnalyzeR is an easy-to use-R package that enables statistical identification of isoform switching from RNA-seq derived quantification
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1254 of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR facilitates integration of many sources of (predicted) annotation such as Open
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1255 Reading Frame (ORF/CDS), protein domains (via Pfam), signal peptides (via SignalP), Intrinsically Disordered Regions (IDR, via NetSurfP-2 or IUPred2A),
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1256 coding potential (via CPAT or CPC2) and sensitivity to Non-sense Mediated Decay (NMD) and more. The combination of identified isoform switches and
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1257 their annotation enables IsoformSwitchAnalyzeR to predict potential functional consequences of the identified isoform switches — such as loss of
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1258 protein domains — thereby identifying isoform switches of particular interest. Lastly, IsoformSwitchAnalyzeR provides article-ready visualization
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1259 methods for isoform switches for individual genes as well as both summary statistics and visualization of the genome-wide changes/consequences of
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1260 isoform switches, their consequences and the associated alternative splicing.
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1261
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1262 -----
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1263
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1264 .. class:: infomark
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1265
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1266 Differential isoform expression (DIE) and differential isoform usage (DIU)
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1267
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1268 Differential isoform expression (DIE) and differential isoform usage (DIU) are related but distinct concepts. DIE assesses the difference of
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1269 absolute expression in isoform level. In contrast, DIU assesses the difference of relative expression in isoform level. For example, if the
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1270 expression of two isoforms of one gene are 10 and 20 in control and 50 and 100 in case, then there is DIE but no DIU because the relative
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1271 expression of the first isoform is 1/3 in both case and control.
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1272
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1273 -----
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1274
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1275 .. class:: infomark
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1276
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1277 ORF identification methods (novel isoform analysis)
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1278
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1279 - Longest: Identifies the longest ORF in the transcript (after filtering via minORFlength). This approach is similar to what the CPAT tool uses in it is analysis of coding potential.
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1280 - LongestAnnotated: Identifies the longest ORF (after filtering via minORFlength) downstream of an annotated translation start site (which are supplied via the cds argument).
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1281 - Longest.AnnotatedWhenPossible: A merge between "longestAnnotated" and "longest". For all isoforms where CDS start positions from known isoform overlap, only these CDS starts are considered and the longest ORF is annotated (similar to "longestAnnotated"). All isoforms without any overlapping CDS start sites they will be analysed with the "longest" approach.
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1282 - MostUpstream: Identifies the most upstream ORF in the transcript (after filtering via minORFlength).
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1283 - MostUpstreamAnnoated: Identifies the ORF (after filtering via minORFlength) downstream of the most upstream overlapping annotated translation start site (supplied via the cds argument).
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1284
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1285 ]]></help>
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1286 <expand macro="citations" />
f3fefb6d8254 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 2c61e4c6151000201dd9a8323722a380bc235380 iuc parents: diff changeset	1287 </tool>

Mercurial > repos > iuc > isoformswitchanalyzer

annotate isoformswitchanalyzer.xml @ 7:d3377a16d881 draft default tip