multiqc: multiqc.xml annotate

annotate multiqc.xml @ 10:ce0f144f4835 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit e22f6c00774c9ec9f29773eba43fd509d55031e4

author	iuc
date	Sun, 05 Aug 2018 18:26:28 -0400
parents	df99138d2776
children	f0ec41881020

rev	line source
10 ce0f144f4835 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit e22f6c00774c9ec9f29773eba43fd509d55031e4 iuc parents: 9 diff changeset	1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.1">
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	2 <description>aggregate results from bioinformatics analyses into a single report</description>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	3 <macros>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	4 <token name="@WRAPPER_VERSION@">1.5</token>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	5 <token name="@ESCAPE_IDENTIFIER@">
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	6 <![CDATA[
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	7 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	8 ]]></token>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	9 <token name="@CHECK_LN_FILE@">
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	10 <![CDATA[
9 df99138d2776 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 31d721c19f5681dfe542dd23185c06c8f29f1945 iuc parents: 8 diff changeset	11 #if $file_path in $file_paths
df99138d2776 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 31d721c19f5681dfe542dd23185c06c8f29f1945 iuc parents: 8 diff changeset	12 #set $file_path += '_' + str($file_paths.count($file_path))
df99138d2776 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 31d721c19f5681dfe542dd23185c06c8f29f1945 iuc parents: 8 diff changeset	13 #end if
df99138d2776 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 31d721c19f5681dfe542dd23185c06c8f29f1945 iuc parents: 8 diff changeset	14 #set $file_paths += [$file_path]
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	15 grep -q "$pattern" $file \|\| die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	16 ln -s '$file' '$file_path' &&
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	17 ]]></token>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	18 <token name="@CREATE_REPEAT_DIR_1@">
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	19 <![CDATA[
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	20 #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	21 mkdir '$repeat_dir' &&
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	22 ]]></token>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	23 <token name="@CREATE_REPEAT_DIR_2@">
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	24 <![CDATA[
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	25 #set repeat_dir = os.path.join($software_dir, str($repeat2.type.type) + '_' + str($j))
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	26 mkdir '$repeat_dir' &&
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	27 ]]></token>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	28 <token name="@LN_FILES@">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	29 <![CDATA[
9 df99138d2776 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 31d721c19f5681dfe542dd23185c06c8f29f1945 iuc parents: 8 diff changeset	30 #set file_paths = []
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	31 #for $file in $repeat.software_cond.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	32 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	33 #set file_path = os.path.join($software_dir, str($identifier))
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	34 @CHECK_LN_FILE@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	35 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	36 ]]></token>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	37 <token name="@LN_2_FILES@">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	38 <![CDATA[
9 df99138d2776 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 31d721c19f5681dfe542dd23185c06c8f29f1945 iuc parents: 8 diff changeset	39 #set file_paths = []
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	40 @CREATE_REPEAT_DIR_1@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	41 #for $file in $repeat2.input
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	42 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	43 #set file_path = os.path.join($repeat_dir, str($identifier))
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	44 @CHECK_LN_FILE@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	45 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	46 ]]></token>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	47 <token name="@LN_3_FILES@">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	48 <![CDATA[
9 df99138d2776 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 31d721c19f5681dfe542dd23185c06c8f29f1945 iuc parents: 8 diff changeset	49 #set file_paths = []
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	50 #for $file in $repeat2.type.input
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	51 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	52 #set file_path = os.path.join($repeat_dir, str($identifier))
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	53 @CHECK_LN_FILE@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	54 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	55 ]]></token>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	56 </macros>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	57 <requirements>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	58 <requirement type="package" version="@WRAPPER_VERSION@">multiqc</requirement>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	59 </requirements>
4 e4574a4d09d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit cb4a49f04475c7f6e2d304ded739c63db9f29724 iuc parents: 3 diff changeset	60 <version_command>multiqc --version</version_command>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	61 <command detect_errors="aggressive">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	62 <![CDATA[
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	63 #import re
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	64 #import os
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	65
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	66 die() { echo "$@" 1>&2 ; exit 1; } &&
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	67
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	68 mkdir multiqc_WDir &&
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	69
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	70 #set $configfile="F"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	71
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	72 #for $i, $repeat in enumerate( $results )
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	73 #set software_dir = os.path.join('multiqc_WDir', str($repeat.software_cond.software) + '_' + str($i))
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	74 mkdir $software_dir &&
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	75
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	76 #if str($repeat.software_cond.software) == "bamtools"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	77 #set $pattern = "Stats for BAM file(s)"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	78 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	79 #elif str($repeat.software_cond.software) == "bcftools"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	80 #set $pattern = "This file was produced by bcftools stats"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	81 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	82 #elif str($repeat.software_cond.software) == "bismark"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	83 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	84 @CREATE_REPEAT_DIR_1@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	85 #if str($repeat2.type) == "align"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	86 #for $file in $repeat2.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	87 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	88 #set file_path = os.path.join($repeat_dir, str($identifier) + '_SE_report.txt')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	89 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	90 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	91 #elif str($repeat2.type) == "dedup"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	92 #for $file in $repeat2.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	93 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	94 #set file_path = os.path.join($repeat_dir, str($identifier) + '_deduplication_report.txt')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	95 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	96 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	97 #elif str($repeat2.type) == "meth_extract"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	98 #for $file in $repeat2.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	99 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	100 #set file_path = os.path.join($repeat_dir, str($identifier) + '_splitting_report.txt')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	101 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	102 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	103 #elif str($repeat2.type) == "m_bias"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	104 #for $file in $repeat2.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	105 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	106 #set file_path = os.path.join($repeat_dir, str($identifier) + '_M-bias.txt')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	107 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	108 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	109 #elif str($repeat2.type) == "bam2nuc"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	110 #for $file in $repeat2.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	111 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	112 #set file_path = os.path.join($repeat_dir, str($identifier) + '.nucleotide_stats.txt')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	113 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	114 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	115 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	116 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	117 #elif str($repeat.software_cond.software) == "bowtie2"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	118 #set $pattern = "reads; of these:"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	119 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	120 #elif str($repeat.software_cond.software) == "busco"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	121 ## Searches for files "short_summary_[samplename].txt"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	122 #for $file in $repeat.software_cond.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	123 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	124 #set file_path = os.path.join($software_dir, 'short_summary_' + str($identifier))
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	125 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	126 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	127 #elif str($repeat.software_cond.software) == "cutadapt"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	128 #set $pattern = "This is cutadapt"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	129 #for $file in $repeat.software_cond.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	130 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	131 #set file_path = os.path.join($software_dir, str($identifier) + '.txt')
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	132 ln -s '$file' '$file_path' &&
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	133 ## replace header for old cutadapt release
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	134 sed -i.old 's/You are running/This is/' '$file_path' &&
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	135 grep -q "$pattern" '$file_path' \|\| die "'$pattern' or 'You are running cutadapt' not found in the file" &&
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	136 #end for
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	137 #elif str($repeat.software_cond.software) == "deeptools"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	138 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	139 #if str($repeat2.type) == "bamPEFragmentSize"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	140 #set $pattern = "Frag."
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	141 @LN_2_FILES@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	142 #elif str($repeat2.type) == "estimateReadFiltering"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	143 #set $pattern = "Internally-determined Duplicate"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	144 @LN_2_FILES@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	145 #elif str($repeat2.type) == "plotCoverageStdout"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	146 #set $pattern = "sample"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	147 @LN_2_FILES@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	148 #elif str($repeat2.type) == "plotCoverageOutRawCounts"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	149 #set $pattern = "#plotCoverage --outRawCounts"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	150 @LN_2_FILES@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	151 #elif str($repeat2.type) == "plotEnrichment"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	152 #set $pattern = "featureReadCount"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	153 @LN_2_FILES@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	154 #elif str($repeat2.type) == "plotFingerprintOutRawCounts"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	155 #set $pattern = "#plotFingerprint --outRawCounts"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	156 @LN_2_FILES@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	157 #end if
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	158 #end for
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	159 #elif str($repeat.software_cond.software) == "fastqc"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	160 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	161 @CREATE_REPEAT_DIR_1@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	162 #if str($repeat2.type) == "data"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	163 #for $k, $file in enumerate($repeat2.input)
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	164 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	165 #set file_path = os.path.join($file_dir, 'fastqc_data.txt')
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	166 mkdir '$file_dir' &&
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	167 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	168 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	169 #elif str($repeat2.type) == "theoretical_gc"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	170 #for $file in $repeat2.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	171 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	172 #set file_path = os.path.join($repeat_dir, str($identifier) + '_fastqc_theoretical_gc')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	173 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	174 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	175 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	176 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	177 #elif str($repeat.software_cond.software) == "featureCounts"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	178 #for $file in $repeat.software_cond.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	179 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	180 #set file_prefix = os.path.join($software_dir, str($identifier))
5 5746cb5cf08d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 36465d526cea3d061724952bb6cf63ee8dd069bf iuc parents: 4 diff changeset	181 if grep -qw Status '$file'; then
5746cb5cf08d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 36465d526cea3d061724952bb6cf63ee8dd069bf iuc parents: 4 diff changeset	182 ln -s '$file' '${file_prefix}.summary';
5746cb5cf08d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 36465d526cea3d061724952bb6cf63ee8dd069bf iuc parents: 4 diff changeset	183 else
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	184 echo -e 'Status\t${identifier}' > '${file_prefix}.summary';
5 5746cb5cf08d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 36465d526cea3d061724952bb6cf63ee8dd069bf iuc parents: 4 diff changeset	185 cat '$file' >> '${file_prefix}.summary';
5746cb5cf08d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 36465d526cea3d061724952bb6cf63ee8dd069bf iuc parents: 4 diff changeset	186 fi &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	187 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	188 #elif str($repeat.software_cond.software) == "flexbar"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	189 #set $pattern = "flexible barcode and adapter removal"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	190 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	191 #elif str($repeat.software_cond.software) == "gatk"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	192 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	193 #if str($repeat2.type) == "varianteval"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	194 #set $pattern = "#:GATKTable:TiTvVariantEvaluator"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	195 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	196 #elif str($repeat2.type) == "base_recalibrator"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	197 #set $pattern = "#:GATKTable:Arguments:Recalibration"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	198 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	199 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	200 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	201 #elif str($repeat.software_cond.software) == "hicup"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	202 #for $file in $repeat.software_cond.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	203 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	204 #set file_path = os.path.join($software_dir, 'HiCUP_summary_report_' + str($identifier))
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	205 ln -s '${file}' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	206 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	207 #elif str($repeat.software_cond.software) == "hisat2"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	208 #set $pattern = "HISAT2 summary stats:"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	209 @LN_FILES@
6 01237d721a9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 iuc parents: 5 diff changeset	210 #elif str($repeat.software_cond.software) == "hicexplorer"
01237d721a9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 iuc parents: 5 diff changeset	211 #set $pattern = "Min rest. site distance"
01237d721a9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 iuc parents: 5 diff changeset	212 @LN_FILES@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	213 #elif str($repeat.software_cond.software) == "htseq"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	214 #set $pattern = "__too_low_aQual"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	215 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	216 #elif str($repeat.software_cond.software) == "kallisto"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	217 #set $pattern = "finding pseudoalignments for the reads"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	218 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	219 #elif str($repeat.software_cond.software) == "picard"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	220 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	221 #if str($repeat2.type) == "alignment_metrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	222 #set $pattern = "picard.analysis.AlignmentSummaryMetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	223 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	224 #elif str($repeat2.type) == "basedistributionbycycle"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	225 #set $pattern = "picard.analysis.BaseDistributionByCycleMetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	226 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	227 #elif str($repeat2.type) == "gcbias"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	228 #set $pattern = "picard.analysis.GcBias"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	229 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	230 #elif str($repeat2.type) == "hsmetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	231 #set $pattern = "picard.analysis.directed.HsMetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	232 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	233 #elif str($repeat2.type) == "insertsize"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	234 #set $pattern = "picard.analysis.InsertSizeMetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	235 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	236 #elif str($repeat2.type) == "markdups"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	237 #set $pattern = "picard.sam.DuplicationMetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	238 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	239 #elif str($repeat2.type) == "oxogmetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	240 #set $pattern = "picard.analysis.CollectOxoGMetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	241 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	242 #elif str($repeat2.type) == "pcr_metrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	243 #set $pattern = "picard.analysis.directed.TargetedPcrMetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	244 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	245 #elif str($repeat2.type) == "rnaseqmetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	246 #set $pattern = "Collect"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	247 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	248 #elif str($repeat2.type) == "rrbs_metrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	249 #set $pattern = "picard.analysis.RrbsSummaryMetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	250 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	251 #elif str($repeat2.type) == "wgs_metrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	252 #set $pattern = "picard.analysis.CollectWgsMetrics$WgsMetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	253 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	254 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	255 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	256 #elif str($repeat.software_cond.software) == "prokka"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	257 #set $pattern = "contigs:"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	258 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	259 #elif str($repeat.software_cond.software) == "quast"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	260 #for $k, $file in enumerate($repeat.software_cond.input)
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	261 #set file_dir = os.path.join($software_dir, 'file_' + str($k))
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	262 #set file_path = os.path.join($file_dir, 'report.tsv')
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	263 mkdir '$file_dir' &&
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	264 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	265 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	266 #elif str($repeat.software_cond.software) == "rsem"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	267 #for $file in $repeat.software_cond.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	268 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	269 #set file_path = os.path.join($software_dir, str($identifier) + '.cnt')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	270 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	271 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	272 #elif str($repeat.software_cond.software) == "rseqc"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	273 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	274 @CREATE_REPEAT_DIR_2@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	275 #if str($repeat2.type.type) == "bam_stat"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	276 #set $pattern = "Proper-paired reads map to different chrom:"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	277 @LN_3_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	278 #elif str($repeat2.type.type) == "gene_body_coverage"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	279 #for $k, $file in enumerate($repeat2.type.input)
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	280 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.geneBodyCoverage.txt')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	281 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	282 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	283 #elif str($repeat2.type.type) == "inner_distance"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	284 #for $k, $file in enumerate($repeat2.type.input)
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	285 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.inner_distance_freq.txt')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	286 ln -s '${file}' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	287 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	288 #elif str($repeat2.type.type) == "junction_annotation"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	289 #set $pattern = "Partial Novel Splicing Junctions:"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	290 @LN_3_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	291 #elif str($repeat2.type.type) == "read_gc"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	292 #for $k, $file in enumerate($repeat2.type.input)
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	293 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.GC.xls')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	294 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	295 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	296 #elif str($repeat2.type.type) == "junction_annotation"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	297 #set $pattern = "Group Total_bases Tag_count Tags/Kb"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	298 @LN_3_FILES@
7 467486f1c568 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d iuc parents: 6 diff changeset	299 #elif str($repeat2.type.type) == "read_distribution"
467486f1c568 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d iuc parents: 6 diff changeset	300 #set $pattern = "Group Total_bases Tag_count Tags/Kb"
467486f1c568 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d iuc parents: 6 diff changeset	301 @LN_3_FILES@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	302 #elif str($repeat2.type.type) == "read_duplication_pos"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	303 #for $k, $file in enumerate($repeat2.type.input)
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	304 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.pos.DupRate.xls')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	305 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	306 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	307 #elif str($repeat2.type.type) == "infer_experiment"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	308 #set $pattern = "Fraction of reads explained by"
10 ce0f144f4835 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit e22f6c00774c9ec9f29773eba43fd509d55031e4 iuc parents: 9 diff changeset	309 #for $file in $repeat2.type.input
ce0f144f4835 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit e22f6c00774c9ec9f29773eba43fd509d55031e4 iuc parents: 9 diff changeset	310 @ESCAPE_IDENTIFIER@
ce0f144f4835 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit e22f6c00774c9ec9f29773eba43fd509d55031e4 iuc parents: 9 diff changeset	311 #set file_path = os.path.join($repeat_dir, str($identifier))
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	312 grep -q "$pattern" $file \|\| die "'$pattern' not found in the file" &&
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	313 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	314 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	315 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	316 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	317 #elif str($repeat.software_cond.software) == "salmon"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	318 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	319 @CREATE_REPEAT_DIR_2@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	320 #if str($repeat2.type.type) == "meta"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	321 #for $k, $file in enumerate($repeat2.type.input)
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	322 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	323 #set file_path = os.path.join($file_dir, 'meta_info.json')
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	324 mkdir '$file_dir' &&
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	325 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	326 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	327 #elif str($repeat2.type.type) == "fld"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	328 #for $k, $file in enumerate($repeat2.type.input)
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	329 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	330 #set file_path = os.path.join($file_dir,'flenDist.txt')
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	331 mkdir '$file_dir' &&
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	332 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	333 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	334 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	335 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	336 #elif str($repeat.software_cond.software) == "samblaster"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	337 #set $pattern = "samblaster: Version"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	338 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	339 #elif str($repeat.software_cond.software) == "samtools"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	340 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	341 @CREATE_REPEAT_DIR_2@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	342 #if str($repeat2.type.type) == "stats"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	343 #set $pattern = "This file was produced by samtools stats"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	344 @LN_3_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	345 #elif str($repeat2.type.type) == "flagstat"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	346 #set $pattern = "in total (QC-passed reads + QC-failed reads)"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	347 @LN_3_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	348 #elif str($repeat2.type.type) == "idxstats"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	349 #for $file in $repeat2.type.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	350 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	351 #set file_path = os.path.join($repeat_dir, str($identifier) + '_idxstat')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	352 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	353 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	354 #elif str($repeat2.type.type) == "rmdup"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	355 #set $pattern = "[bam_rmdup"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	356 @LN_3_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	357 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	358 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	359 #elif str($repeat.software_cond.software) == "snpeff"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	360 #set $pattern = "SnpEff_version"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	361 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	362 #elif str($repeat.software_cond.software) == "sortmerna"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	363 #set $pattern = "Minimal SW score based on E-value"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	364 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	365 #else if str($repeat.software_cond.software) == "star":
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	366 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	367 @CREATE_REPEAT_DIR_2@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	368 #if str($repeat2.type.type) == "log"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	369 #for $file in $repeat2.type.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	370 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	371 #set file_path = os.path.join($repeat_dir, str($identifier) + '_Log.final.out')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	372 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	373 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	374 #elif str($repeat2.type.type) == "genecounts"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	375 #for $file in $repeat2.type.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	376 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	377 #set file_path = os.path.join($repeat_dir, str($identifier) + '_ReadsPerGene.out.tab')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	378 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	379 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	380 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	381 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	382 #elif str($repeat.software_cond.software) == "tophat"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	383 #for $file in $repeat.software_cond.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	384 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	385 #set file_path = os.path.join($software_dir, str($identifier) + 'align_summary.txt')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	386 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	387 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	388 #elif str($repeat.software_cond.software) == "trimmomatic"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	389 #set $pattern = "Trimmomatic"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	390 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	391 #elif str($repeat.software_cond.software) == "vcftools"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	392 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	393 @CREATE_REPEAT_DIR_2@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	394 #if str($repeat2.type.type) == "relatedness2"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	395 #for $file in $repeat2.type.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	396 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	397 #set file_path = os.path.join($repeat_dir, str($identifier) + '.relatedness2')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	398 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	399 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	400 #elif str($repeat2.type) == "tstv_by_count"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	401 #for $file in $repeat2.type.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	402 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	403 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.count')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	404 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	405 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	406 #elif str($repeat2.type) == "tstv_by_qual"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	407 #for $file in $repeat2.type.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	408 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	409 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.qual')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	410 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	411 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	412 #elif str($repeat2.type) == "tstv_summary"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	413 #for $file in $repeat2.type.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	414 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	415 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.summary')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	416 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	417 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	418 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	419 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	420 #else if str($repeat.software_cond.software) == "custom_content":
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	421 #set $configfile = "T"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	422 #for $j, $file in enumerate( $repeat.software_cond.input )
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	423 #set file_path = os.path.join($software_dir, 'file_' + str($i) + '_' + str($j))
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	424 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	425 more $file &&
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	426 #end for
1 6999173dc0c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 110247de01764a544371d07eaed0308429a47daa iuc parents: 0 diff changeset	427 #end if
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	428 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	429
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	430 multiqc multiqc_WDir
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	431 --filename "report"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	432
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	433 #if str($title)
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	434 --title "$title"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	435 #end if
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	436 #if str($comment)
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	437 --comment "$comment"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	438 #end if
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	439
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	440 #if $configfile == "T"
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	441 --config '$multiqc_config'
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	442 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	443 ]]></command>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	444 <configfiles>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	445 <configfile name="multiqc_config">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	446 <![CDATA[
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	447 custom_data:
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	448 #for $i, $repeat in enumerate( $results )
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	449 #if str($repeat.software_cond.software) == "custom_content"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	450 section_$i:
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	451 file_format: 'tsv'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	452 section_name: '$repeat.software_cond.section_name'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	453 title: '$repeat.software_cond.title'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	454 description: '$repeat.software_cond.description'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	455 plot_type: '$repeat.software_cond.plot_type'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	456 pconfig:
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	457 id: 'section_${i}_${repeat.software_cond.plot_type}'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	458 ylab: '$repeat.software_cond.ylab'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	459 xlab: '$repeat.software_cond.xlab'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	460 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	461 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	462 sp:
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	463 #for $i, $repeat in enumerate( $results )
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	464 #if str($repeat.software_cond.software) == "custom_content"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	465 section_$i:
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	466 fn: 'file_${i}_*'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	467 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	468 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	469 ]]></configfile>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	470 </configfiles>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	471 <inputs>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	472 <repeat name="results" title="Results" min="1">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	473 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	474 <param name="software" type="select" label="Which tool was used generate logs?" help="Software name">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	475 <!--<option value="adapterRemoval">Adapter Removal</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	476 <!--<option value="afterqc">AfterQC</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	477 <option value="bamtools">Bamtools</option>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	478 <!--<option value="bbmap">BBMap</option>-->
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	479 <option value="bcftools">Bcftools</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	480 <!--<option value="bcl2fastq">bcl2fastq</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	481 <!--<option value="biobloomtools">BioBloom Tools</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	482 <option value="bismark">Bismark</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	483 <!--<option value="bowtie1">Bowtie 1</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	484 <option value="bowtie2">Bowtie 2</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	485 <option value="busco">BUSCO</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	486 <!--<option value="clusterflow">Cluster Flow</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	487 <option value="cutadapt">Cutadapt/Trim Galore!</option>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	488 <!--<option value="clipandmerge">ClipAndMerge</option>-->
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	489 <!--<option value="conpair">Conpair</option>-->
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	490 <!--<option value="dedup">DeDup</option>-->
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	491 <option value="deeptools">deepTools</option>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	492 <!--<option value="disambiguate">Disambiguate</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	493 <!--<option value="fastq_screen">FastQ Screen</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	494 <option value="fastqc">FastQC</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	495 <option value="featureCounts">featureCounts</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	496 <option value="flexbar">Flexbar</option>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	497 <option value="gatk">GATK</option>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	498 <!--<option value="goleft_indexcov">goleft indexcov</option>-->
6 01237d721a9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 iuc parents: 5 diff changeset	499 <option value="hicexplorer">HiCExplorer</option>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	500 <!--<option value="hicup">HiCUP</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	501 <option value="hisat2">HISAT2</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	502 <!--<option value="homer">HOMER</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	503 <option value="htseq">HTSeq</option>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	504 <!--<option value="interop">InterOp</option>-->
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	505 <!--<option value="jellyfish">Jellyfish</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	506 <option value="kallisto">Kallisto</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	507 <!--<option value="leehom">leeHom</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	508 <!--<option value="macs2">MACS2</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	509 <!--<option value="methylQA">methylQA</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	510 <!--<option value="peddy">Peddy</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	511 <option value="picard">Picard</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	512 <!--<option value="preseq">Preseq</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	513 <option value="prokka">Prokka</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	514 <!--<option value="qorts">QoRTs</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	515 <!--<option value="qualimap">Qualimap (BamQC or RNASeq output)</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	516 <option value="quast">QUAST</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	517 <!--<option value="rna_seqc">RNA-SeQC</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	518 <!--<option value="rsem">RSEM (rsem-calculate-regex output)</option>-->
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	519 <option value="rseqc">RSeQC</option>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	520 <!--<option value="salmon">Salmon</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	521 <option value="samblaster">Samblaster</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	522 <option value="samtools">Samtools</option>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	523 <!--<option value="sargasso">Sargasso</option>-->
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	524 <!--<option value="skewer">Skewer</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	525 <!--<option value="slamdunk">Slamdunk</option>-->
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	526 <option value="snpeff">SnpEff</option>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	527 <option value="sortmerna">SortMeRNA</option>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	528 <option value="star">STAR</option>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	529 <!--<option value="supernova">Supernova</option>-->
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	530 <!--<option value="theta2">THeTA2</option>-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	531 <option value="tophat">TopHat2</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	532 <option value="trimmomatic">Trimmomatic</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	533 <option value="vcftools">VCFTools</option>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	534 <!--<option value="verifybamid">VerifyBAMID</option>-->
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	535 <!--Custom-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	536 <option value="custom_content">Custom Content</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	537 </param>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	538 <when value="bamtools">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	539 <param name="input" type="data" format="txt" multiple="true" label="Output of BAMtools" help="It should contain 'Stats for BAM file(s)'"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	540 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	541 <when value="bcftools">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	542 <param name="input" type="data" format="txt" multiple="true" label="Output of BAMtools" help="It should contain 'This file was produced by bcftools stats'"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	543 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	544 <when value="bismark">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	545 <repeat name="output" title="Bismark output" min="1">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	546 <param name="type" type="select" label="Type of Bismark output?">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	547 <option value="align">Alignment file</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	548 <option value="dedup">Deduplication file</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	549 <option value="meth_extract">Methylation file</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	550 <option value="m_bias">m_bias file</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	551 <option value="bam2nuc">bam2nuc file</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	552 </param>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	553 <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	554 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	555 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	556 <when value="bowtie2">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	557 <param name="input" type="data" format="txt" multiple="true" label="Output of Bowtie 2" help="It should contain 'reads; of these:'"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	558 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	559 <when value="busco">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	560 <param name="input" type="data" format="txt" multiple="true" label="Output of BUSCO"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	561 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	562 <when value="cutadapt">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	563 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Cutadapt" help="It should contain 'This is cutadapt' or 'You are running cutadapt'"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	564 </when>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	565 <when value="deeptools">
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	566 <repeat name="output" title="deepTools output" min="1">
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	567 <param name="type" type="select" label="deepTool used to generate the output?">
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	568 <option value="bamPEFragmentSize">bamPEFragmentSize</option>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	569 <option value="estimateReadFiltering">estimateReadFiltering</option>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	570 <option value="plotCoverageStdout">plotCoverageStdout</option>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	571 <option value="plotCoverageOutRawCounts">plotCoverageOutRawCounts</option>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	572 <option value="plotEnrichment">plotEnrichment</option>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	573 <option value="plotFingerprintOutRawCounts">plotFingerprintOutRawCounts</option>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	574 <option value="plotFingerprintOutQualityMetrics">plotFingerprintOutQualityMetrics</option>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	575 </param>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	576 <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	577 </repeat>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	578 </when>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	579 <when value="fastqc">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	580 <repeat name="output" title="FastQC output" min="1">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	581 <param name="type" type="select" label="Type of FastQC output?">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	582 <option value="data">Raw data</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	583 <option value="theoretical_gc">Theorectical GC</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	584 </param>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	585 <param name="input" type="data" format="txt" multiple="true" label="FastQC output">
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	586 <validator type="expression" message="MultiQC does not accept the HTML report generated by FastQC, only the Raw Data">value is not None and value.extension != "html"</validator>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	587 </param>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	588 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	589 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	590 <when value="featureCounts">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	591 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of FeatureCounts"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	592 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	593 <when value="flexbar">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	594 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Flexbar" help="It should contain 'Flexbar - flexible barcode and adapter removal'"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	595 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	596 <when value="gatk">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	597 <repeat name="output" title="GATK output" min="1">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	598 <param name="type" type="select" label="Type of GATK output?">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	599 <option value="varianteval">Variant eval file</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	600 <option value="base_recalibrator">Base recalibrator file</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	601 </param>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	602 <param name="input" type="data" format="txt" multiple="true" label="GATK output"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	603 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	604 </when>
6 01237d721a9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 iuc parents: 5 diff changeset	605 <when value="hicexplorer">
01237d721a9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 iuc parents: 5 diff changeset	606 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HiCExplorer" help="It should contain 'Min rest. site distance'"/>
01237d721a9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 iuc parents: 5 diff changeset	607 </when>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	608 <when value="hisat2">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	609 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HISAT2" help="It should contain 'HISAT2 summary stats:'"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	610 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	611 <when value="htseq">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	612 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HTSeq" help="It should contain '__too_low_aQual'"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	613 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	614 <when value="kallisto">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	615 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Kallisto" help="It should contain '[quant] finding pseudoalignments for the reads'"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	616 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	617 <when value="picard">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	618 <repeat name="output" title="Picard output" min="1">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	619 <param name="type" type="select" label="Type of Picard output?">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	620 <option value="alignment_metrics">Alignment metrics</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	621 <option value="basedistributionbycycle">Base distribution by cycle</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	622 <option value="gcbias">GC bias</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	623 <option value="hsmetrics">HS Metrics</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	624 <option value="insertsize">Insert size</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	625 <option value="markdups">Markdups</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	626 <option value="oxogmetrics">Oxog metrics</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	627 <option value="pcr_metrics">PCR metrics</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	628 <option value="rnaseqmetrics">RNA Seq metrics</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	629 <option value="rrbs_metrics">RRBS metrics</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	630 <option value="wgs_metrics">WGS metrics</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	631 </param>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	632 <param name="input" type="data" format="txt" multiple="true" label="Picard output"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	633 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	634 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	635 <when value="prokka">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	636 <param name="input" type="data" format="txt" multiple="true" label="Output of Prokka" help="It should contain 'contigs:'"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	637 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	638 <when value="quast">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	639 <param name="input" type="data" format="tabular,tsv" multiple="true" label="Output of Quast"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	640 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	641 <when value="rseqc">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	642 <repeat name="output" title="RSeQC output" min="1">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	643 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	644 <param name="type" type="select" label="Type of RSeQC output?">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	645 <option value="bam_stat">bam_stat</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	646 <option value="gene_body_coverage">gene_body_coverage</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	647 <option value="infer_experiment">infer_experiment</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	648 <option value="inner_distance">inner_distance</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	649 <option value="junction_annotation">junction_annotation</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	650 <option value="junction_saturation">junction_saturation</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	651 <option value="read_distribution">read_distribution</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	652 <option value="read_duplication_pos">read_duplication_pos</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	653 <option value="read_gc">read_gc</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	654 </param>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	655 <when value="bam_stat">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	656 <param name="input" type="data" format="txt,tabular" multiple="true" label="RSeQC bam_stat output" help="It should contain 'Proper-paired reads map to different chrom:'"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	657 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	658 <when value="gene_body_coverage">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	659 <param name="input" type="data" format="txt" multiple="true" label="RSeQC gene_body_coverage output"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	660 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	661 <when value="infer_experiment">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	662 <param name="input" type="data" format="txt" multiple="true" label="RSeQC infer_experiment output" help="It should contain 'Fraction of reads explained by'"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	663 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	664 <when value="inner_distance">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	665 <param name="input" type="data" format="txt,xls,tabular" multiple="true" label="RSeQC inner_distance output"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	666 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	667 <when value="junction_annotation">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	668 <param name="input" type="data" format="txt,xls,tabular" multiple="true" label="RSeQC junction_annotation output" help="It should contain 'Partial Novel Splicing Junctions:'"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	669 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	670 <when value="junction_saturation">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	671 <param name="input" type="data" format="txt" multiple="true" label="RSeQC junction_saturation output"/>
1 6999173dc0c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 110247de01764a544371d07eaed0308429a47daa iuc parents: 0 diff changeset	672 </when>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	673 <when value="read_distribution">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	674 <param name="input" type="data" format="txt,xls,tabular" multiple="true" label="RSeQC read_distribution output" help="It should contain 'Group Total_bases Tag_count Tags/Kb'"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	675 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	676 <when value="read_duplication_pos">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	677 <param name="input" type="data" format="csv,xls,tabular" multiple="true" label="RSeQC read_duplication_pos output"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	678 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	679 <when value="read_gc">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	680 <param name="input" type="data" format="csv,xls,tabular" multiple="true" label="RSeQC read_gc output"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	681 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	682 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	683 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	684 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	685 <when value="samblaster">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	686 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Samblaster" help="It should contain 'samblaster: Version'"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	687 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	688 <when value="samtools">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	689 <repeat name="output" title="Samtools output" min="1">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	690 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	691 <param name="type" type="select" label="Type of Samtools output?">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	692 <option value="stats">stats</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	693 <option value="flagstat">flagstat</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	694 <option value="idxstats">idxstats</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	695 <option value="rmdup">rmdup</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	696 </param>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	697 <when value="stats">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	698 <param name="input" type="data" format="txt" multiple="true" label="Samtools stats output" help="It should contain 'This file was produced by samtools stats'"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	699 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	700 <when value="flagstat">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	701 <param name="input" type="data" format="txt" multiple="true" label="Samtools flagstat output" help="It should contain 'in total (QC-passed reads + QC-failed reads)'"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	702 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	703 <when value="idxstats">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	704 <param name="input" type="data" format="txt" multiple="true" label="Samtools idxstats output"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	705 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	706 <when value="rmdup">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	707 <param name="input" type="data" format="txt" multiple="true" label="Samtools rmdup output" help="It should contain '[bam_rmdup'"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	708 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	709 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	710 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	711 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	712 <when value="sortmerna">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	713 <param name="input" type="data" format="txt" multiple="true" label="Log file of SortMeRNA" help="It should contain 'Minimal SW score based on E-value'"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	714 </when>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	715 <when value="snpeff">
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	716 <param name="input" type="data" format="csv" multiple="true" label="Output of SnpEff"/>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	717 </when>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	718 <when value="star">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	719 <repeat name="output" title="STAR output" min="1">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	720 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	721 <param name="type" type="select" label="Type of STAR output?">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	722 <option value="log">Log</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	723 <option value="genecounts">Gene counts</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	724 </param>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	725 <when value="log">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	726 <param name="input" type="data" format="txt" multiple="true" label="STAR log output"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	727 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	728 <when value="genecounts">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	729 <param name="input" type="data" format="tabular,tsv" multiple="true" label="STAR gene count output"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	730 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	731 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	732 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	733 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	734 <when value="tophat">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	735 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of TopHat2"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	736 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	737 <when value="trimmomatic">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	738 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Trimmomatic" help="It should contain 'TTrimmomatic'"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	739 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	740 <when value="vcftools">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	741 <repeat name="output" title="VCFTools output" min="1">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	742 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	743 <param name="type" type="select" label="Type of VCFTools output?">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	744 <option value="relatedness2">relatedness2</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	745 <option value="tstv_by_count">tstv_by_count</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	746 <option value="tstv_by_qual">tstv_by_qual</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	747 <option value="tstv_summary">tstv_summary</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	748 </param>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	749 <when value="relatedness2">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	750 <param name="input" type="data" format="txt" multiple="true" label="VCFTools relatedness2 output"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	751 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	752 <when value="tstv_by_count">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	753 <param name="input" type="data" format="tabular,tsv" multiple="true" label="VCFTools TsTV count output"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	754 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	755 <when value="tstv_by_qual">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	756 <param name="input" type="data" format="tabular" multiple="true" label="VCFTools TsTV qual output"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	757 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	758 <when value="tstv_summary">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	759 <param name="input" type="data" format="txt" multiple="true" label="VCFTools TsTV summary output"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	760 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	761 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	762 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	763 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	764 <when value="custom_content">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	765 <param argument="plot_type" label="The plot type to visualise the data with" type="select">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	766 <option value="linegraph">linegraph</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	767 <option value="bargraph">bargraph</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	768 <option value="scatter">scatter</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	769 <option value="generalstats">generalstats</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	770 <option value="table">table</option>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	771 </param>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	772 <param argument="section_name" label="Section name" type="text" help="Nice name used for the report section header" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	773 <param argument="title" label="Title" type="text" help="Plot title" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	774 <param argument="description" label="Description" type="text" help="Introductory text to be printed under the section header" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	775 <param argument="xlab" label="X axis label" type="text" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	776 <param argument="ylab" label="Y axis label" type="text" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	777 <param name="input" type="data" format="tabular,tsv" multiple="true" label="Data files"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	778 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	779 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	780 </repeat>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	781 <param name="title" type="text" value="" optional="true" label="Report title" help="It is printed as page header"/>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	782 <param name="comment" type="text" value="" optional="true" label="Custom comment" help="It will be printed at the top of the report"/>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	783 <param name="saveLog" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output the multiQC log file?" help="This is mostly useful for debugging purposes"/>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	784 <param name="saveLog" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output the multiQC log file?" help="This is mostly useful for debugging purposes"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	785 </inputs>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	786 <outputs>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	787 <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage" />
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	788 <data name="log" format="txt" from_work_dir="report_data/multiqc.log" label="${tool.name} on ${on_string}: Log">
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	789 <filter>saveLog</filter>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	790 </data>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	791 <collection name="stats" type="list" label="${tool.name} on ${on_string}: Stats">
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	792 <discover_datasets pattern="multiqc_(?P<designation>.+)\.txt" format="tabular" directory="report_data" />
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	793 </collection>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	794 </outputs>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	795 <tests>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	796 <test>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	797 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	798 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	799 <param name="software" value="cutadapt" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	800 <param name="input" value="cutadapt.txt" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	801 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	802 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	803 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	804 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	805 <param name="software" value="fastqc" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	806 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	807 <param name="type" value="data"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	808 <param name="input" value="fastqc_1.txt,fastqc_2.txt"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	809 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	810 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	811 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	812 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	813 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	814 <param name="software" value="flexbar" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	815 <param name="input" value="flexbar.txt" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	816 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	817 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	818 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	819 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	820 <param name="software" value="sortmerna" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	821 <param name="input" value="sortmerna.txt" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	822 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	823 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	824 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	825 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	826 <param name="software" value="trimmomatic" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	827 <param name="input" value="trimmomatic.txt" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	828 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	829 </repeat>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	830 <param name="title" value="Title of the report"/>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	831 <param name="comment" value="Commment for the report"/>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	832 <param name="saveLog" value="True"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	833 <output name="html_report">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	834 <assert_contents>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	835 <has_text text="Title of the report" />
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	836 <has_text text="Commment for the report" />
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	837 <has_text text="cutadapt_plot" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	838 <has_text text="fastqc_seq_heatmap_key_t" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	839 <has_text text="flexbar_plot" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	840 <has_text text="sortmerna-detailed-plot" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	841 <has_text text="trimmomatic_plot" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	842 </assert_contents>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	843 </output>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	844 <output name="log" file="pre_alignment_soft_log.txt" compare="sim_size"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	845 <output_collection name="stats" type="list">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	846 <element name="cutadapt" file="cutadapt_stats.tabular" compare="sim_size" delta="10"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	847 <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	848 <element name="flexbar" file="flexbar_stats.tabular" compare="sim_size" delta="10"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	849 <element name="general_stats" file="pre_alignment_soft_stats.tabular" compare="sim_size" delta="30"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	850 <element name="sortmerna" file="sortmerna_stats.tabular" compare="sim_size" delta="30"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	851 <element name="trimmomatic" file="trimmomatic_stats.tabular" compare="sim_size" delta="0"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	852 </output_collection>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	853 </test>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	854 <test>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	855 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	856 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	857 <param name="software" value="bismark" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	858 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	859 <param name="type" value="align"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	860 <param name="input" value="bismark.txt"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	861 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	862 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	863 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	864 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	865 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	866 <param name="software" value="bowtie2" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	867 <param name="input" value="bowtie2_1.txt,bowtie2_2.txt" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	868 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	869 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	870 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	871 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	872 <param name="software" value="hisat2" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	873 <param name="input" value="hisat2_1.txt,hisat2_2.txt" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	874 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	875 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	876 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	877 <conditional name="software_cond">
6 01237d721a9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 iuc parents: 5 diff changeset	878 <param name="software" value="hicexplorer" />
9 df99138d2776 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 31d721c19f5681dfe542dd23185c06c8f29f1945 iuc parents: 8 diff changeset	879 <param name="input" value="hicexplorer1.log,hicexplorer1.log,hicexplorer2.log" />
6 01237d721a9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 iuc parents: 5 diff changeset	880 </conditional>
01237d721a9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 iuc parents: 5 diff changeset	881 </repeat>
01237d721a9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 iuc parents: 5 diff changeset	882 <repeat name="results">
01237d721a9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 iuc parents: 5 diff changeset	883 <conditional name="software_cond">
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	884 <param name="software" value="kallisto" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	885 <param name="input" value="kallisto_1.txt,kallisto_2.txt" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	886 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	887 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	888 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	889 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	890 <param name="software" value="star" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	891 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	892 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	893 <param name="type" value="log"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	894 <param name="input" value="star_log.txt" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	895 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	896 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	897 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	898 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	899 <param name="type" value="genecounts"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	900 <param name="input" value="star_counts.txt" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	901 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	902 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	903 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	904 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	905 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	906 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	907 <param name="software" value="tophat" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	908 <param name="input" value="tophat.txt" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	909 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	910 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	911 <param name="saveLog" value="False"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	912 <output name="html_report">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	913 <assert_contents>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	914 <has_text text="bismark-alignment" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	915 <has_text text="bowtie2_se_plot" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	916 <has_text text="hisat2_se_plot" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	917 <has_text text="kallisto_alignment" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	918 <has_text text="star_alignment_plot" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	919 <has_text text="tophat_alignment" />
6 01237d721a9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 iuc parents: 5 diff changeset	920 <has_text text="hicexplorer" />
9 df99138d2776 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 31d721c19f5681dfe542dd23185c06c8f29f1945 iuc parents: 8 diff changeset	921 <has_text text="hicexplorer1_log_1" />
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	922 </assert_contents>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	923 </output>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	924 <output_collection name="stats" type="list">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	925 <element name="bismark_alignment" file="bismark_stats.tabular" compare="sim_size" delta="10"/>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	926 <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="20"/>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	927 <element name="general_stats" file="aligner_soft_stats.tabular" compare="sim_size" delta="50"/>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	928 <element name="hisat2" file="hisat2_stats.tabular" compare="sim_size" delta="20"/>
6 01237d721a9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 iuc parents: 5 diff changeset	929 <!-- <element name="hicexplorer" file="hicexplorer_stats.tabular" compare="sim_size" delta="0"/> -->
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	930 <element name="kallisto" file="kallisto_stats.tabular" compare="sim_size" delta="10"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	931 <element name="star" file="star_stats.tabular" compare="sim_size" delta="10"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	932 <element name="tophat.txt" file="tophat_stats.tabular" compare="sim_size" delta="10"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	933 </output_collection>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	934 </test>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	935 <test>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	936 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	937 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	938 <param name="software" value="bamtools" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	939 <param name="input" value="bamtools.txt" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	940 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	941 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	942 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	943 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	944 <param name="software" value="bcftools" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	945 <param name="input" value="bcftools.txt" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	946 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	947 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	948 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	949 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	950 <param name="software" value="busco" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	951 <param name="input" value="busco.txt" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	952 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	953 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	954 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	955 <conditional name="software_cond">
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	956 <param name="software" value="deeptools" />
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	957 <repeat name="output">
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	958 <param name="type" value="bamPEFragmentSize"/>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	959 <param name="input" value="deeptools_bamPEFragmentSize.txt"/>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	960 </repeat>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	961 <repeat name="output">
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	962 <param name="type" value="estimateReadFiltering"/>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	963 <param name="input" value="deeptools_estimateReadFiltering.txt"/>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	964 </repeat>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	965 <repeat name="output">
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	966 <param name="type" value="plotCoverageStdout"/>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	967 <param name="input" value="deeptools_plotCoverageStdout.txt"/>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	968 </repeat>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	969 <repeat name="output">
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	970 <param name="type" value="plotCoverageOutRawCounts"/>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	971 <param name="input" value="deeptools_plotCoverageOutRawCounts.txt"/>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	972 </repeat>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	973 <repeat name="output">
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	974 <param name="type" value="plotEnrichment"/>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	975 <param name="input" value="deeptools_plotEnrichment.txt"/>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	976 </repeat>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	977 <repeat name="output">
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	978 <param name="type" value="plotFingerprintOutRawCounts"/>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	979 <param name="input" value="deeptools_plotFingerprintOutRawCounts.txt"/>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	980 </repeat>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	981 </conditional>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	982 </repeat>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	983 <repeat name="results">
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	984 <conditional name="software_cond">
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	985 <param name="software" value="featureCounts" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	986 <param name="input" value="featureCounts.txt" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	987 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	988 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	989 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	990 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	991 <param name="software" value="gatk" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	992 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	993 <param name="type" value="base_recalibrator"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	994 <param name="input" value="gatk_BaseRecalibrator.txt"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	995 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	996 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	997 <param name="type" value="varianteval"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	998 <param name="input" value="gatk_varianteval.txt"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	999 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1000 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1001 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1002 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1003 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1004 <param name="software" value="htseq" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1005 <param name="input" value="htseq.txt" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1006 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1007 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1008 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1009 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1010 <param name="software" value="picard" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1011 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1012 <param name="type" value="gcbias"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1013 <param name="input" value="picard_collectGcBias.txt"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1014 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1015 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1016 <param name="type" value="insertsize"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1017 <param name="input" value="picard_CollectInsertSizeMetrics.txt"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1018 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1019 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1020 <param name="type" value="markdups"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1021 <param name="input" value="picard_MarkDuplicates.txt"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1022 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1023 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1024 <param name="type" value="basedistributionbycycle"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1025 <param name="input" value="picard_CollectBaseDistributionByCycle.txt"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1026 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1027 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1028 <param name="type" value="rnaseqmetrics"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1029 <param name="input" value="picard_CollectRnaSeqMetrics.txt"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1030 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1031 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1032 <param name="type" value="alignment_metrics"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1033 <param name="input" value="picard_CollectAlignmentSummaryMetrics.txt"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1034 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1035 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1036 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1037 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1038 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1039 <param name="software" value="prokka" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1040 <param name="input" value="prokka_1.txt,prokka_2.txt" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1041 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1042 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1043 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1044 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1045 <param name="software" value="quast" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1046 <param name="input" value="quast.tsv" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1047 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1048 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1049 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1050 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1051 <param name="software" value="rseqc" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1052 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1053 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1054 <param name="type" value="read_gc"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1055 <param name="input" value="rseqc.txt"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1056 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1057 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1058 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1059 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1060 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1061 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1062 <param name="software" value="samblaster" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1063 <param name="input" value="samblaster.txt" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1064 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1065 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1066 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1067 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1068 <param name="software" value="samtools" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1069 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1070 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1071 <param name="type" value="stats"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1072 <param name="input" value="samtools_stats.txt"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1073 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1074 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1075 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1076 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1077 <param name="type" value="flagstat"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1078 <param name="input" value="samtools_flagstat.txt"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1079 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1080 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1081 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1082 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1083 <param name="type" value="idxstats"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1084 <param name="input" value="samtools_idxstats.txt"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1085 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1086 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1087 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1088 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1089 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1090 <conditional name="software_cond">
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1091 <param name="software" value="snpeff" />
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1092 <param name="input" value="snpeff.csv" />
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1093 </conditional>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1094 </repeat>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1095 <repeat name="results">
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1096 <conditional name="software_cond">
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1097 <param name="software" value="vcftools" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1098 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1099 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1100 <param name="type" value="tstv_by_qual"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1101 <param name="input" value="vcftools.txt"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1102 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1103 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1104 <param name="input" value="vcftools.txt" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1105 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1106 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1107 <output name="html_report">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1108 <assert_contents>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1109 <has_text text="bamtools-stats" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1110 <has_text text="bcftools_stats_indel-lengths" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1111 <has_text text="busco-lineage-fungi_odb9" />
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1112 <has_text text="deeptools" />
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1113 <has_text text="featureCounts_assignment_plot" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1114 <has_text text="gatk_varianteval_variant_plot" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1115 <has_text text="htseq_assignment_plot" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1116 <has_text text="picard_aligned_reads" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1117 <has_text text="picard-rna-assignment" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1118 <has_text text="picard-markduplicates" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1119 <has_text text="picard-insertsize" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1120 <has_text text="picard-gcbias" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1121 <has_text text="prokka_plot" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1122 <has_text text="samblaster_duplicates" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1123 <has_text text="quast-stats" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1124 <has_text text="samtools-flagstat-dp" />
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1125 <has_text text="snpeff" />
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1126 </assert_contents>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1127 </output>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1128 <output_collection name="stats" type="list">
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1129 <element name="bamtools_stats" file="bamtools_stats.tabular" compare="sim_size" delta="10"/>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1130 <element name="bcftools_stats" file="bcftools_stats.tabular" compare="sim_size" delta="0"/>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1131 <element name="busco" file="busco_stats.tabular" compare="sim_size" delta="10"/>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1132 <element name="featureCounts" file="featureCounts_stats.tabular" compare="sim_size" delta="25"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1133 <element name="gatk_varianteval" file="gatk_varianteval_stats.tabular" compare="sim_size" delta="20"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1134 <element name="general_stats" file="post_aligner_soft_stats.tabular" compare="sim_size" delta="25"/>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1135 <element name="htseq" file="htseq_stats.tabular" compare="sim_size" delta="10"/>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1136 <element name="picard_AlignmentSummaryMetrics" file="picard_AlignmentSummaryMetrics_stats.tabular" compare="sim_size" delta="0"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1137 <element name="picard_RnaSeqMetrics" file="picard_RnaSeqMetrics_stats.tabular" compare="sim_size" delta="40"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1138 <element name="picard_baseContent" file="picard_baseContent_stats.tabular" compare="sim_size" delta="50"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1139 <element name="picard_dups" file="picard_dups_stats.tabular" compare="sim_size" delta="0"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1140 <element name="picard_insertSize" file="picard_insertSize_stats.tabular" compare="sim_size" delta="0"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1141 <element name="prokka" file="prokka_stats.tabular" compare="sim_size" delta="0"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1142 <element name="quast" file="quast_stats.tabular" compare="sim_size" delta="0"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1143 <element name="samblaster" file="samblaster_stats.tabular" compare="sim_size" delta="0"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1144 <element name="samtools_flagstat">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1145 <assert_contents>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1146 <has_text text="samtools_flagstat" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1147 <has_text text="mapped_passed" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1148 <has_text text="20689039" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1149 </assert_contents>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1150 </element>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1151 <element name="samtools_stats" file="samtools_stats_stats.tabular" compare="sim_size" delta="15"/>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1152 <element name="snpeff" file="snpeff_stats.tabular" compare="sim_size" delta="10"/>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1153 </output_collection>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1154 </test>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1155 <test>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1156 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1157 <conditional name="software_cond">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1158 <param name="software" value="custom_content" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1159 <param name="cc_select" value="manual" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1160 <param name="plot_type" value="linegraph" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1161 <param name="section_name" value="BPC" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1162 <param name="title" value="Base peak chromatogram" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1163 <param name="description" value="Sum of intensity (Y) of the most intense peaks at each retention time(X)" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1164 <param name="xlab" value="Retention Time" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1165 <param name="ylab" value="Base Peak Intensity" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1166 <param name="input" value="cc_ko15.bpc.tab,cc_wt15.bpc.tab" />
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1167 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1168 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1169 <output name="html_report" file="report_manual_custom_content.html" compare="sim_size"/>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1170 </test>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1171 </tests>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1172 <help><![CDATA[
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1173 What it does
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1174
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1175 `MultiQC <http://multiqc.info/>`_ aggregates results from bioinformatics analyses across many samples into a single report. It takes results of multiple analyses and creates a report that can be viewed as a single beautiful web-page. It's a general use tool, perfect for summarizing the output from numerous bioinformatics tools.
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1176
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1177 Inputs
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1178
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1179 MultiQC takes software output summaries/logs and creates a single report from them. You need to tell the tool which software was used to generate the report. This is done using the Software name dropdown. At present only the Galaxy tools found in the ToolShed produce logs that can used with MultiQC
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1180
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1181 ----
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1182
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1183 The first integration of this tool was made by Cyril Monjeaud and Yvan Le Bras (`Enancio <http://enancio.fr/>`_ and Rennes GenOuest Bio-informatics Core Facility). It is now maintained by the `Intergalactic Utilities Commission <https://galaxyproject.org/iuc>`_.
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1184 ]]></help>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1185 <citations>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1186 <citation type="doi">10.1093/bioinformatics/btw354</citation>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1187 </citations>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1188 </tool>

Mercurial > repos > iuc > multiqc

annotate multiqc.xml @ 10:ce0f144f4835 draft