multiqc: multiqc.xml annotate

annotate multiqc.xml @ 21:75c93c70d094 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"

author	iuc
date	Tue, 02 Mar 2021 21:08:49 +0000
parents	c1a4b5f3b432
children	9a913cdee30e

rev	line source
21 75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy1">
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>
19 f7985e0479b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b" iuc parents: 18 diff changeset	4 <token name="@WRAPPER_VERSION@">1.9</token>
8 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]
21 75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	15 grep -q '$pattern' $file \|\| die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
8 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>
20 c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	56 <xml name="element_assert" token_name="" token_lines="" token_columns="" token_text="">
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	57 <element name="@NAME@">
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	58 <assert_contents>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	59 <has_n_columns n="@COLUMNS@"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	60 <has_n_lines n="@LINES@"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	61 <has_text text="@TEXT@"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	62 <yield/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	63 </assert_contents>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	64 </element>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	65 </xml>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	66 </macros>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	67 <requirements>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	68 <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	69 </requirements>
4 e4574a4d09d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit cb4a49f04475c7f6e2d304ded739c63db9f29724 iuc parents: 3 diff changeset	70 <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	71 <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	72 <![CDATA[
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	73 #import re
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	74 #import os
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	75
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	76 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	77
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	78 mkdir multiqc_WDir &&
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	79
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	80 #set $configfile="F"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	81
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	82 #for $i, $repeat in enumerate( $results )
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	83 #set software_dir = os.path.join('multiqc_WDir', str($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	84 mkdir $software_dir &&
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	85
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	86 #if str($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	87 #set $pattern = "Stats for BAM file(s)"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	88 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	89 #elif str($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	90 #set $pattern = "This file was produced by bcftools stats"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	91 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	92 #elif str($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	93 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	94 @CREATE_REPEAT_DIR_1@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	95 #if str($repeat2.type) == "align"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	96 #for $file in $repeat2.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	97 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	98 #set file_path = os.path.join($repeat_dir, str($identifier) + '_SE_report.txt')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	99 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	100 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	101 #elif str($repeat2.type) == "dedup"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	102 #for $file in $repeat2.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	103 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	104 #set file_path = os.path.join($repeat_dir, str($identifier) + '_deduplication_report.txt')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	105 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	106 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	107 #elif str($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	108 #for $file in $repeat2.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	109 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	110 #set file_path = os.path.join($repeat_dir, str($identifier) + '_splitting_report.txt')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	111 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	112 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	113 #elif str($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	114 #for $file in $repeat2.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	115 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	116 #set file_path = os.path.join($repeat_dir, str($identifier) + '_M-bias.txt')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	117 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	118 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	119 #elif str($repeat2.type) == "bam2nuc"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	120 #for $file in $repeat2.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	121 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	122 #set file_path = os.path.join($repeat_dir, str($identifier) + '.nucleotide_stats.txt')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	123 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	124 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	125 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	126 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	127 #elif str($repeat.software_cond.software) == "bowtie2"
17 5e33b465d8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc" iuc parents: 16 diff changeset	128 #set $pattern = "% overall alignment rate"
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	129 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	130 #elif str($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	131 ## 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	132 #for $file in $repeat.software_cond.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	133 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	134 #set file_path = os.path.join($software_dir, 'short_summary_' + str($identifier))
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	135 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	136 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	137 #elif str($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	138 #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	139 #for $file in $repeat.software_cond.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	140 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	141 #set file_path = os.path.join($software_dir, str($identifier) + '.txt')
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	142 ln -s '$file' '$file_path' &&
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	143 ## replace header for old cutadapt release
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	144 sed -i.old 's/You are running/This is/' '$file_path' &&
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	145 grep -q "$pattern" '$file_path' \|\| die "'$pattern' or 'You are running cutadapt' not found in the file" &&
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	146 #end for
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	147 #elif str($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	148 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	149 #if str($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	150 #set $pattern = "Frag."
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	151 @LN_2_FILES@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	152 #elif str($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	153 #set $pattern = "Internally-determined Duplicate"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	154 @LN_2_FILES@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	155 #elif str($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	156 #set $pattern = "sample"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	157 @LN_2_FILES@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	158 #elif str($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	159 #set $pattern = "#plotCoverage --outRawCounts"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	160 @LN_2_FILES@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	161 #elif str($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	162 #set $pattern = "featureReadCount"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	163 @LN_2_FILES@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	164 #elif str($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	165 #set $pattern = "#plotFingerprint --outRawCounts"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	166 @LN_2_FILES@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	167 #end if
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	168 #end for
12 1c2db0054039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 11 diff changeset	169 #elif str($repeat.software_cond.software) == "fastp"
1c2db0054039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 11 diff changeset	170 #set $pattern = "report_title"
1c2db0054039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 11 diff changeset	171 #for $file in $repeat.software_cond.input
1c2db0054039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 11 diff changeset	172 @ESCAPE_IDENTIFIER@
1c2db0054039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 11 diff changeset	173 #set file_path = os.path.join($software_dir, str($identifier) + 'fastp.json')
1c2db0054039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 11 diff changeset	174 ln -s '$file' '$file_path' &&
1c2db0054039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 11 diff changeset	175 grep -q "$pattern" '$file_path' \|\| die "'$pattern' or 'report_title' not found in the file" &&
1c2db0054039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 11 diff changeset	176 #end for
0 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) == "fastqc"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	178 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	179 @CREATE_REPEAT_DIR_1@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	180 #if str($repeat2.type) == "data"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	181 #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	182 #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	183 #set file_path = os.path.join($file_dir, 'fastqc_data.txt')
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	184 mkdir '$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	185 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	186 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	187 #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	188 #for $file in $repeat2.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	189 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	190 #set file_path = os.path.join($repeat_dir, str($identifier) + '_fastqc_theoretical_gc')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	191 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	192 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	193 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	194 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	195 #elif str($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	196 #for $file in $repeat.software_cond.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	197 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	198 #set file_prefix = os.path.join($software_dir, str($identifier))
5 5746cb5cf08d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 36465d526cea3d061724952bb6cf63ee8dd069bf iuc parents: 4 diff changeset	199 if grep -qw Status '$file'; then
5746cb5cf08d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 36465d526cea3d061724952bb6cf63ee8dd069bf iuc parents: 4 diff changeset	200 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	201 else
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	202 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	203 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	204 fi &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	205 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	206 #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	207 #set $pattern = "flexible barcode and adapter removal"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	208 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	209 #elif str($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	210 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	211 #if str($repeat2.type) == "varianteval"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	212 #set $pattern = "#:GATKTable:TiTvVariantEvaluator"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	213 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	214 #elif str($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	215 #set $pattern = "#:GATKTable:Arguments:Recalibration"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	216 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	217 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	218 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	219 #elif str($repeat.software_cond.software) == "hicup"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	220 #for $file in $repeat.software_cond.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	221 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	222 #set file_path = os.path.join($software_dir, 'HiCUP_summary_report_' + str($identifier))
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	223 ln -s '${file}' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	224 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	225 #elif str($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	226 #set $pattern = "HISAT2 summary stats:"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	227 @LN_FILES@
6 01237d721a9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 iuc parents: 5 diff changeset	228 #elif str($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	229 #set $pattern = "Min rest. site distance"
01237d721a9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 iuc parents: 5 diff changeset	230 @LN_FILES@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	231 #elif str($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	232 #set $pattern = "__too_low_aQual"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	233 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	234 #elif str($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	235 #set $pattern = "finding pseudoalignments for the reads"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	236 @LN_FILES@
11 f0ec41881020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 iuc parents: 10 diff changeset	237 #elif str($repeat.software_cond.software) == "macs2"
f0ec41881020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 iuc parents: 10 diff changeset	238 #set $pattern = "# This file is generated by MACS"
f0ec41881020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 iuc parents: 10 diff changeset	239 #for $file in $repeat.software_cond.input
f0ec41881020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 iuc parents: 10 diff changeset	240 @ESCAPE_IDENTIFIER@
f0ec41881020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 iuc parents: 10 diff changeset	241 #set file_path = os.path.join($software_dir, str($identifier) + '_peaks.xls')
f0ec41881020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 iuc parents: 10 diff changeset	242 grep -q "$pattern" $file \|\| die "'$pattern' not found in the file" &&
f0ec41881020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 iuc parents: 10 diff changeset	243 ln -s '$file' '$file_path' &&
f0ec41881020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 iuc parents: 10 diff changeset	244 #end for
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	245 #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	246 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	247 #if str($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	248 #set $pattern = "picard.analysis.AlignmentSummaryMetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	249 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	250 #elif str($repeat2.type) == "basedistributionbycycle"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	251 #set $pattern = "picard.analysis.BaseDistributionByCycleMetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	252 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	253 #elif str($repeat2.type) == "gcbias"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	254 #set $pattern = "picard.analysis.GcBias"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	255 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	256 #elif str($repeat2.type) == "hsmetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	257 #set $pattern = "picard.analysis.directed.HsMetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	258 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	259 #elif str($repeat2.type) == "insertsize"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	260 #set $pattern = "picard.analysis.InsertSizeMetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	261 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	262 #elif str($repeat2.type) == "markdups"
17 5e33b465d8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc" iuc parents: 16 diff changeset	263 #set $pattern = "MarkDuplicates"
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	264 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	265 #elif str($repeat2.type) == "oxogmetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	266 #set $pattern = "picard.analysis.CollectOxoGMetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	267 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	268 #elif str($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	269 #set $pattern = "picard.analysis.directed.TargetedPcrMetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	270 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	271 #elif str($repeat2.type) == "rnaseqmetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	272 #set $pattern = "Collect"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	273 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	274 #elif str($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	275 #set $pattern = "picard.analysis.RrbsSummaryMetrics"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	276 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	277 #elif str($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	278 #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	279 @LN_2_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	280 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	281 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	282 #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	283 #set $pattern = "contigs:"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	284 @LN_FILES@
21 75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	285 #elif str($repeat.software_cond.software) == "pycoqc"
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	286 #set $pattern = "\"pycoqc\":"
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	287 @LN_FILES@
16 bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	288 #elif str($repeat.software_cond.software) == "qualimap"
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	289 #for $file in $repeat.software_cond.input
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	290 #if re.search("genome_results", str($file.element_identifier))
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	291 sample="\$(grep 'bam file = ' $file \| sed 's/bam file = //g' \| sed 's: ::g')" &&
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	292 dir_name="$software_dir/\${sample}" &&
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	293 mkdir -p \${dir_name} &&
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	294 filepath_1="\${dir_name}/genome_results.txt" &&
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	295 ln -sf '$file' \${filepath_1} &&
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	296 #elif re.search("coverage_histogram", str($file.element_identifier))
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	297 nested_dir_name="\${dir_name}/raw_data_qualimapReport/" &&
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	298 mkdir -p \${nested_dir_name} &&
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	299 filepath_2="\${nested_dir_name}/coverage_histogram.txt" &&
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	300 ln -sf '$file' \${filepath_2} &&
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	301 #elif re.search("gc-content_distribution", str($file.element_identifier))
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	302 nested_dir_name="\${dir_name}/raw_data_qualimapReport/" &&
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	303 mkdir -p \${nested_dir_name} &&
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	304 filepath_3="\${nested_dir_name}/mapped_reads_gc-content_distribution.txt" &&
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	305 ln -sf '$file' \${filepath_3} &&
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	306 #else
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	307 #pass
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	308 #end if
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	309 #end for
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	310 #elif str($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	311 #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	312 #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	313 #set file_path = os.path.join($file_dir, 'report.tsv')
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	314 mkdir '$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	315 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	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) == "rsem"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	318 #for $file in $repeat.software_cond.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	319 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	320 #set file_path = os.path.join($software_dir, str($identifier) + '.cnt')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	321 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	322 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	323 #elif str($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	324 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	325 @CREATE_REPEAT_DIR_2@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	326 #if str($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	327 #set $pattern = "Proper-paired reads map to different chrom:"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	328 @LN_3_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	329 #elif str($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	330 #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	331 #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	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 #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	335 #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	336 #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	337 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	338 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	339 #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	340 #set $pattern = "Partial Novel Splicing Junctions:"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	341 @LN_3_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	342 #elif str($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	343 #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	344 #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	345 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	346 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	347 #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	348 #set $pattern = "Group Total_bases Tag_count Tags/Kb"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	349 @LN_3_FILES@
7 467486f1c568 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d iuc parents: 6 diff changeset	350 #elif str($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	351 #set $pattern = "Group Total_bases Tag_count Tags/Kb"
467486f1c568 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d iuc parents: 6 diff changeset	352 @LN_3_FILES@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	353 #elif str($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	354 #for $k, $file in enumerate($repeat2.type.input)
20 c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	355 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.pos.DupRate.xls')
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	356 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	357 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	358 #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	359 #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	360 #for $file in $repeat2.type.input
ce0f144f4835 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit e22f6c00774c9ec9f29773eba43fd509d55031e4 iuc parents: 9 diff changeset	361 @ESCAPE_IDENTIFIER@
ce0f144f4835 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit e22f6c00774c9ec9f29773eba43fd509d55031e4 iuc parents: 9 diff changeset	362 #set file_path = os.path.join($repeat_dir, str($identifier))
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	363 grep -q "$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	364 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	365 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	366 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	367 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	368 #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	369 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	370 @CREATE_REPEAT_DIR_2@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	371 #if str($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	372 #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	373 #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	374 #set file_path = os.path.join($file_dir, 'meta_info.json')
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	375 mkdir '$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	376 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	377 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	378 #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	379 #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	380 #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	381 #set file_path = os.path.join($file_dir,'flenDist.txt')
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	382 mkdir '$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	383 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	384 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	385 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	386 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	387 #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	388 #set $pattern = "samblaster: Version"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	389 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	390 #elif str($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	391 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	392 @CREATE_REPEAT_DIR_2@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	393 #if str($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	394 #set $pattern = "This file was produced by samtools stats"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	395 @LN_3_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	396 #elif str($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	397 #set $pattern = "in total (QC-passed reads + QC-failed reads)"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	398 @LN_3_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	399 #elif str($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	400 #for $file in $repeat2.type.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	401 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	402 #set file_path = os.path.join($repeat_dir, str($identifier) + '_idxstat')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	403 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	404 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	405 #elif str($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	406 #set $pattern = "[bam_rmdup"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	407 @LN_3_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	408 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	409 #end for
13 161f4383df15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b iuc parents: 12 diff changeset	410 #elif str($repeat.software_cond.software) == "slamdunk"
161f4383df15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b iuc parents: 12 diff changeset	411 #set $pattern = "# slamdunk"
161f4383df15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b iuc parents: 12 diff changeset	412 @LN_FILES@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	413 #elif str($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	414 #set $pattern = "SnpEff_version"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	415 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	416 #elif str($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	417 #set $pattern = "Minimal SW score based on E-value"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	418 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	419 #else if str($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	420 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	421 @CREATE_REPEAT_DIR_2@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	422 #if str($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	423 #for $file in $repeat2.type.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	424 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	425 #set file_path = os.path.join($repeat_dir, str($identifier) + '_Log.final.out')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	426 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	427 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	428 #elif str($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	429 #for $file in $repeat2.type.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	430 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	431 #set file_path = os.path.join($repeat_dir, str($identifier) + '_ReadsPerGene.out.tab')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	432 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	433 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	434 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	435 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	436 #elif str($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	437 #for $file in $repeat.software_cond.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	438 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	439 #set file_path = os.path.join($software_dir, str($identifier) + 'align_summary.txt')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	440 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	441 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	442 #elif str($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	443 #set $pattern = "Trimmomatic"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	444 @LN_FILES@
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	445 #elif str($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	446 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	447 @CREATE_REPEAT_DIR_2@
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	448 #if str($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	449 #for $file in $repeat2.type.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	450 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	451 #set file_path = os.path.join($repeat_dir, str($identifier) + '.relatedness2')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	452 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	453 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	454 #elif str($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	455 #for $file in $repeat2.type.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	456 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	457 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.count')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	458 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	459 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	460 #elif str($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	461 #for $file in $repeat2.type.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	462 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	463 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.qual')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	464 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	465 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	466 #elif str($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	467 #for $file in $repeat2.type.input
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	468 @ESCAPE_IDENTIFIER@
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	469 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.summary')
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	470 ln -s '$file' '$file_path' &&
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	471 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	472 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	473 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	474 #else if str($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	475 #set $configfile = "T"
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	476 #for $j, $file in enumerate( $repeat.software_cond.input )
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	477 #set file_path = os.path.join($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	478 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	479 more $file &&
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	480 #end for
1 6999173dc0c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 110247de01764a544371d07eaed0308429a47daa iuc parents: 0 diff changeset	481 #end if
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	482 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	483
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	484 multiqc multiqc_WDir
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	485 --filename "report"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	486
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	487 #if str($title)
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	488 --title "$title"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	489 #end if
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	490 #if str($comment)
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	491 --comment "$comment"
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	492 #end if
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	493
15 3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	494 $flat
19 f7985e0479b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b" iuc parents: 18 diff changeset	495 $export
15 3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	496
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	497 #if $configfile == "T"
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	498 --config '$multiqc_config'
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	499 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	500 ]]></command>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	501 <configfiles>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	502 <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	503 <![CDATA[
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	504 custom_data:
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	505 #for $i, $repeat in enumerate( $results )
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	506 #if str($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	507 section_$i:
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	508 file_format: 'tsv'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	509 section_name: '$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	510 title: '$repeat.software_cond.title'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	511 description: '$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	512 plot_type: '$repeat.software_cond.plot_type'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	513 pconfig:
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	514 id: 'section_${i}_${repeat.software_cond.plot_type}'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	515 ylab: '$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	516 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	517 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	518 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	519 sp:
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	520 #for $i, $repeat in enumerate( $results )
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	521 #if str($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	522 section_$i:
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	523 fn: 'file_${i}_*'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	524 #end if
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	525 #end for
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	526 ]]></configfile>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	527 </configfiles>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	528 <inputs>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	529 <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	530 <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	531 <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	532 <!--<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	533 <!--<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	534 <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	535 <!--<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	536 <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	537 <!--<option value="bcl2fastq">bcl2fastq</option>-->
16 bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	538 <!--<option value="biobambam2">biobambam2</option>-->
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	539 <!--<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	540 <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	541 <!--<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	542 <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	543 <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	544 <!--<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	545 <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	546 <!--<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	547 <!--<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	548 <!--<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	549 <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	550 <!--<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	551 <!--<option value="fastq_screen">FastQ Screen</option>-->
12 1c2db0054039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 11 diff changeset	552 <option value="fastp">fastp</option>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	553 <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	554 <option value="featureCounts">featureCounts</option>
16 bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	555 <!--<option value="fgbio">fgbio</option>-->
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	556 <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	557 <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	558 <!--<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	559 <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	560 <!--<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	561 <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	562 <!--<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	563 <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	564 <!--<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	565 <!--<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	566 <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	567 <!--<option value="leehom">leeHom</option>-->
11 f0ec41881020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 iuc parents: 10 diff changeset	568 <option value="macs2">MACS2</option>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	569 <!--<option value="methylQA">methylQA</option>-->
16 bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	570 <!--<option value="mosdepth">mostdepth</option>-->
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	571 <!--<option value="mtnucratio">mtnucratio</option>-->
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	572 <!--<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	573 <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	574 <!--<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	575 <option value="prokka">Prokka</option>
21 75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	576 <option value="pycoqc">PycoQC</option>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	577 <!--<option value="qorts">QoRTs</option>-->
16 bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	578 <option value="qualimap">Qualimap (BamQC or RNASeq output)</option>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	579 <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	580 <!--<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	581 <!--<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	582 <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	583 <!--<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	584 <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	585 <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	586 <!--<option value="sargasso">Sargasso</option>-->
16 bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	587 <!--<option value="seqyclean">SeqyClean</option>-->
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	588 <!--<option value="sexdeterrmine">SexDetErrmine</option>-->
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	589 <!--<option value="skewer">Skewer</option>-->
13 161f4383df15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b iuc parents: 12 diff changeset	590 <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	591 <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	592 <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	593 <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	594 <!--<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	595 <!--<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	596 <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	597 <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	598 <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	599 <!--<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	600 <!--Custom-->
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	601 <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	602 </param>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	603 <when value="bamtools">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	604 <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	605 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	606 <when value="bcftools">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	607 <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	608 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	609 <when value="bismark">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	610 <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	611 <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	612 <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	613 <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	614 <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	615 <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	616 <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	617 </param>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	618 <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	619 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	620 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	621 <when value="bowtie2">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	622 <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	623 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	624 <when value="busco">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	625 <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	626 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	627 <when value="cutadapt">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	628 <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	629 </when>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	630 <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	631 <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	632 <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	633 <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	634 <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	635 <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	636 <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	637 <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	638 <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	639 <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	640 </param>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	641 <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	642 </repeat>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	643 </when>
12 1c2db0054039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 11 diff changeset	644 <when value="fastp">
1c2db0054039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 11 diff changeset	645 <param name="input" type="data" format="json" multiple="true" label="Output of fastp" help="It should be the json report from fastp containing 'report_title'"/>
1c2db0054039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 11 diff changeset	646 </when>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	647 <when value="fastqc">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	648 <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	649 <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	650 <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	651 <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	652 </param>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	653 <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	654 <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	655 </param>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	656 </repeat>
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="featureCounts">
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,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	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="flexbar">
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,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	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="gatk">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	665 <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	666 <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	667 <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	668 <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	669 </param>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	670 <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	671 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	672 </when>
6 01237d721a9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 iuc parents: 5 diff changeset	673 <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	674 <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	675 </when>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	676 <when value="hisat2">
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="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	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="htseq">
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="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	681 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	682 <when value="kallisto">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	683 <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	684 </when>
11 f0ec41881020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 iuc parents: 10 diff changeset	685 <when value="macs2">
f0ec41881020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 iuc parents: 10 diff changeset	686 <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of MACS2" help="It should be a tabular file containing '# This file is generated by MACS'"/>
f0ec41881020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 iuc parents: 10 diff changeset	687 </when>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	688 <when value="picard">
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="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	690 <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	691 <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	692 <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	693 <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	694 <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	695 <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	696 <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	697 <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	698 <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	699 <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	700 <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	701 <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	702 </param>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	703 <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	704 </repeat>
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="prokka">
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="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	708 </when>
21 75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	709 <when value="pycoqc">
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	710 <param name="input" type="data" format="txt,json" multiple="true" label="Output of PycoQC"/>
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	711 </when>
16 bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	712 <when value="qualimap">
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	713 <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of Qualimap BamQC" help="First result input should be genome_coverage (default from tool output). Run the Flatten Collection tool to keep all output in one report" />
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	714 </when>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	715 <when value="quast">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	716 <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	717 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	718 <when value="rseqc">
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="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	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 RSeQC 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="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	723 <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	724 <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	725 <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	726 <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	727 <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	728 <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	729 <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	730 <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	731 </param>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	732 <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	733 <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	734 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	735 <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	736 <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	737 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	738 <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	739 <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	740 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	741 <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	742 <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	743 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	744 <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	745 <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	746 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	747 <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	748 <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	749 </when>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	750 <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	751 <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	752 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	753 <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	754 <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	755 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	756 <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	757 <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	758 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	759 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	760 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	761 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	762 <when value="samblaster">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	763 <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	764 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	765 <when value="samtools">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	766 <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	767 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	768 <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	769 <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	770 <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	771 <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	772 <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	773 </param>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	774 <when value="stats">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	775 <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	776 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	777 <when value="flagstat">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	778 <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	779 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	780 <when value="idxstats">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	781 <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	782 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	783 <when value="rmdup">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	784 <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	785 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	786 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	787 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	788 </when>
13 161f4383df15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b iuc parents: 12 diff changeset	789 <when value="slamdunk">
161f4383df15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b iuc parents: 12 diff changeset	790 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of Slamdunk Alleyoop" help="It should contain '# slamdunk'"/>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	791 </when>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	792 <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	793 <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	794 </when>
13 161f4383df15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b iuc parents: 12 diff changeset	795 <when value="sortmerna">
161f4383df15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b iuc parents: 12 diff changeset	796 <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'"/>
161f4383df15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b iuc parents: 12 diff changeset	797 </when>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	798 <when value="star">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	799 <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	800 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	801 <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	802 <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	803 <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	804 </param>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	805 <when value="log">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	806 <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	807 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	808 <when value="genecounts">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	809 <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	810 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	811 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	812 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	813 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	814 <when value="tophat">
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" 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	816 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	817 <when value="trimmomatic">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	818 <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	819 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	820 <when value="vcftools">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	821 <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	822 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	823 <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	824 <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	825 <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	826 <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	827 <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	828 </param>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	829 <when value="relatedness2">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	830 <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	831 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	832 <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	833 <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	834 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	835 <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	836 <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	837 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	838 <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	839 <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	840 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	841 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	842 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	843 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	844 <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	845 <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	846 <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	847 <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	848 <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	849 <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	850 <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	851 </param>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	852 <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	853 <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	854 <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	855 <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	856 <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	857 <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	858 </when>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	859 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	860 </repeat>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	861 <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	862 <param name="comment" type="text" value="" optional="true" label="Custom comment" help="It will be printed at the top of the report"/>
18 c19b16e5729c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9" iuc parents: 17 diff changeset	863 <param argument="--flat" type="boolean" truevalue="--flat" falsevalue="" checked="false" label="Use only flat plots (non-interactive images)" help="To consume less disk space and resources to display. Used by default when there are 100 or more samples."/>
19 f7985e0479b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b" iuc parents: 18 diff changeset	864 <param argument="--export" type="boolean" truevalue="--export" falsevalue="" checked="false" label="Output the multiQC plots raw data?" help="This will output a file for each plot containing the raw data used to generate the plot"/>
18 c19b16e5729c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9" iuc parents: 17 diff changeset	865 <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	866 </inputs>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	867 <outputs>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	868 <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage" />
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	869 <data name="log" format="txt" from_work_dir="report_data/multiqc.log" label="${tool.name} on ${on_string}: Log">
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	870 <filter>saveLog</filter>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	871 </data>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	872 <collection name="stats" type="list" label="${tool.name} on ${on_string}: Stats">
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	873 <discover_datasets pattern="multiqc_(?P<designation>.+)\.txt" format="tabular" directory="report_data" />
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	874 </collection>
15 3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	875 <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots">
18 c19b16e5729c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9" iuc parents: 17 diff changeset	876 <discover_datasets pattern="mqc_(?P<designation>.+)\.txt" format="tabular" directory="report_data" />
19 f7985e0479b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b" iuc parents: 18 diff changeset	877 <filter>export</filter>
15 3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	878 </collection>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	879 </outputs>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	880 <tests>
18 c19b16e5729c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9" iuc parents: 17 diff changeset	881 <test expect_num_outputs="4">
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	882 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	883 <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	884 <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	885 <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	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">
12 1c2db0054039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 11 diff changeset	890 <param name="software" value="fastp" />
1c2db0054039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 11 diff changeset	891 <param name="input" value="fastp1.json.txt,fastp2.json.txt" />
1c2db0054039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 11 diff changeset	892 </conditional>
1c2db0054039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 11 diff changeset	893 </repeat>
1c2db0054039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 11 diff changeset	894 <repeat name="results">
1c2db0054039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 11 diff changeset	895 <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	896 <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	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 <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	899 <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	900 </repeat>
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 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	904 <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	905 <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	906 <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	907 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	908 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	909 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	910 <conditional name="software_cond">
13 161f4383df15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b iuc parents: 12 diff changeset	911 <param name="software" value="slamdunk" />
161f4383df15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b iuc parents: 12 diff changeset	912 <param name="input" value="slamdunk_summary.txt,slamdunk_reads1_overallrates.csv,slamdunk_reads2_overallrates.csv" />
161f4383df15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b iuc parents: 12 diff changeset	913 </conditional>
161f4383df15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b iuc parents: 12 diff changeset	914 </repeat>
161f4383df15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b iuc parents: 12 diff changeset	915 <repeat name="results">
161f4383df15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b iuc parents: 12 diff changeset	916 <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	917 <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	918 <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	919 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	920 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	921 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	922 <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	923 <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	924 <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	925 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	926 </repeat>
8 e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	927 <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	928 <param name="comment" value="Commment for the report"/>
18 c19b16e5729c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9" iuc parents: 17 diff changeset	929 <param name="flat" value="true"/>
19 f7985e0479b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b" iuc parents: 18 diff changeset	930 <param name="export" value="true"/>
18 c19b16e5729c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9" iuc parents: 17 diff changeset	931 <param name="saveLog" value="true"/>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	932 <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	933 <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	934 <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	935 <has_text text="Commment for the report" />
19 f7985e0479b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b" iuc parents: 18 diff changeset	936 <has_text text="cutadapt_trimmed_sequences_plot" />
12 1c2db0054039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 11 diff changeset	937 <has_text text="An ultra-fast all-in-one FASTQ preprocessor" />
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	938 <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	939 <has_text text="flexbar_plot" />
13 161f4383df15 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b iuc parents: 12 diff changeset	940 <has_text text="a tool to analyze SLAMSeq data" />
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	941 <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	942 <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	943 </assert_contents>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	944 </output>
18 c19b16e5729c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9" iuc parents: 17 diff changeset	945 <output name="log">
c19b16e5729c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9" iuc parents: 17 diff changeset	946 <assert_contents>
c19b16e5729c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9" iuc parents: 17 diff changeset	947 <has_text_matching expression="\[INFO \] MultiQC complete$"/>
c19b16e5729c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9" iuc parents: 17 diff changeset	948 </assert_contents>
c19b16e5729c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9" iuc parents: 17 diff changeset	949 </output>
19 f7985e0479b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b" iuc parents: 18 diff changeset	950 <output_collection name="stats" type="list" count="10">
20 c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	951 <expand macro="element_assert" name="cutadapt" columns="8" lines="2" text="dataset_33"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	952 <expand macro="element_assert" name="fastp" columns="2" lines="3" text="R1_fq"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	953 <expand macro="element_assert" name="fastqc" columns="22" lines="3" text="poulet5_1"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	954 <expand macro="element_assert" name="flexbar" columns="11" lines="2" text="result_right"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	955 <expand macro="element_assert" name="general_stats" columns="20" lines="11" text="bwa-mem-fastq1_fq"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	956 <expand macro="element_assert" name="slamdunk_readrates_plus" columns="13" lines="3" text="slamdunk_reads1_overallrates_csv"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	957 <expand macro="element_assert" name="slamdunk_readrates_minus" columns="13" lines="3" text="slamdunk_reads1_overallrates_csv"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	958 <expand macro="element_assert" name="sortmerna" columns="22" lines="2" text="25839_merged"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	959 <expand macro="element_assert" name="sources" columns="4" lines="7" text="Module"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	960 <expand macro="element_assert" name="trimmomatic" columns="6" lines="2" text="C2"/>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	961 </output_collection>
18 c19b16e5729c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9" iuc parents: 17 diff changeset	962 <output_collection name="plots" type="list" count="29"/>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	963 </test>
18 c19b16e5729c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9" iuc parents: 17 diff changeset	964 <test expect_num_outputs="2">
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	965 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	966 <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	967 <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	968 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	969 <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	970 <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	971 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	972 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	973 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	974 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	975 <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	976 <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	977 <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	978 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	979 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	980 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	981 <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	982 <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	983 <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	984 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	985 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	986 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	987 <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	988 <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	989 <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	990 </conditional>
01237d721a9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 iuc parents: 5 diff changeset	991 </repeat>
01237d721a9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361 iuc parents: 5 diff changeset	992 <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	993 <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	994 <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	995 <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	996 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	997 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	998 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	999 <conditional name="software_cond">
11 f0ec41881020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 iuc parents: 10 diff changeset	1000 <param name="software" value="macs2" />
f0ec41881020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 iuc parents: 10 diff changeset	1001 <param name="input" value="macs_1.txt,macs_2.txt" />
f0ec41881020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 iuc parents: 10 diff changeset	1002 </conditional>
f0ec41881020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 iuc parents: 10 diff changeset	1003 </repeat>
f0ec41881020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 iuc parents: 10 diff changeset	1004 <repeat name="results">
f0ec41881020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 iuc parents: 10 diff changeset	1005 <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	1006 <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	1007 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1008 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1009 <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	1010 <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	1011 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1012 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1013 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1014 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1015 <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	1016 <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	1017 </conditional>
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 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1020 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1021 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1022 <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	1023 <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	1024 <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	1025 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1026 </repeat>
18 c19b16e5729c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9" iuc parents: 17 diff changeset	1027 <param name="saveLog" value="false"/>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1028 <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	1029 <assert_contents>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1030 <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	1031 <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	1032 <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	1033 <has_text text="kallisto_alignment" />
11 f0ec41881020 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 iuc parents: 10 diff changeset	1034 <has_text text="MACS2" />
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1035 <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	1036 <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	1037 <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	1038 <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	1039 </assert_contents>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1040 </output>
20 c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1041 <output_collection name="stats" type="list" count="11">
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1042 <expand macro="element_assert" name="bismark_alignment" columns="21" lines="2" text="bismark_txt_SE_report"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1043 <expand macro="element_assert" name="bowtie2" columns="7" lines="3" text="bowtie2_1_txt"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1044 <expand macro="element_assert" name="cutadapt" columns="8" lines="5" text="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1045 <expand macro="element_assert" name="general_stats" columns="21" lines="19" text="treat2"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1046 <expand macro="element_assert" name="hicexplorer" columns="41" lines="4" text="hicexplorer_3_hicexplorer2_log_small_test_rf"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1047 <expand macro="element_assert" name="hisat2" columns="6" lines="3" text="hisat2_2_txt"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1048 <expand macro="element_assert" name="kallisto" columns="6" lines="3" text="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1049 <expand macro="element_assert" name="macs" columns="11" lines="3" text="treat2"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1050 <expand macro="element_assert" name="sources" columns="4" lines="18" text="Cutadapt"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1051 <expand macro="element_assert" name="star" columns="27" lines="2" text="star_log_txt"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1052 <expand macro="element_assert" name="tophat.txt" columns="9" lines="2" text="tophat_txtalign"/>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1053 </output_collection>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1054 </test>
18 c19b16e5729c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9" iuc parents: 17 diff changeset	1055 <test expect_num_outputs="2">
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1056 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1057 <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	1058 <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	1059 <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	1060 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1061 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1062 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1063 <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	1064 <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	1065 <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	1066 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1067 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1068 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1069 <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	1070 <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	1071 <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	1072 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1073 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1074 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1075 <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	1076 <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	1077 <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	1078 <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	1079 <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	1080 </repeat>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1081 <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	1082 <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	1083 <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	1084 </repeat>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1085 <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	1086 <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	1087 <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	1088 </repeat>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1089 <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	1090 <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	1091 <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	1092 </repeat>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1093 <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	1094 <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	1095 <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	1096 </repeat>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1097 <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	1098 <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	1099 <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	1100 </repeat>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1101 </conditional>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1102 </repeat>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1103 <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	1104 <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	1105 <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	1106 <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	1107 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1108 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1109 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1110 <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	1111 <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	1112 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1113 <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	1114 <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	1115 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1116 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1117 <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	1118 <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	1119 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1120 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1121 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1122 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1123 <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	1124 <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	1125 <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	1126 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1127 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1128 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1129 <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	1130 <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	1131 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1132 <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	1133 <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	1134 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1135 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1136 <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	1137 <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	1138 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1139 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1140 <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	1141 <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	1142 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1143 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1144 <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	1145 <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	1146 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1147 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1148 <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	1149 <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	1150 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1151 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1152 <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	1153 <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	1154 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1155 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1156 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1157 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1158 <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	1159 <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	1160 <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	1161 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1162 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1163 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1164 <conditional name="software_cond">
16 bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	1165 <param name="software" value="qualimap" />
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	1166 <param name="input" value="genome_results.txt" />
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	1167 </conditional>
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	1168 </repeat>
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	1169 <repeat name="results">
bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	1170 <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	1171 <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	1172 <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	1173 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1174 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1175 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1176 <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	1177 <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	1178 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1179 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1180 <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	1181 <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	1182 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1183 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1184 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1185 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1186 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1187 <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	1188 <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	1189 <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	1190 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1191 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1192 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1193 <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	1194 <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	1195 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1196 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1197 <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	1198 <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	1199 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1200 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1201 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1202 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1203 <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	1204 <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	1205 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1206 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1207 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1208 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1209 <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	1210 <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	1211 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1212 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1213 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1214 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1215 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1216 <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	1217 <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	1218 <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	1219 </conditional>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1220 </repeat>
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20 iuc parents: 7 diff changeset	1221 <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	1222 <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	1223 <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	1224 <repeat name="output">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1225 <conditional name="type">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1226 <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	1227 <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	1228 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1229 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1230 <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	1231 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1232 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1233 <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	1234 <assert_contents>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1235 <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	1236 <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	1237 <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	1238 <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	1239 <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	1240 <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	1241 <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	1242 <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	1243 <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	1244 <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	1245 <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	1246 <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	1247 <has_text text="prokka_plot" />
16 bf675f34b056 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" iuc parents: 15 diff changeset	1248 <has_text text="qualimap" />
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1249 <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	1250 <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	1251 <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	1252 <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	1253 </assert_contents>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1254 </output>
20 c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1255 <output_collection name="stats" type="list" count="21">
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1256 <expand macro="element_assert" name="bamtools_stats" columns="20" lines="2" text="bamtools_txt"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1257 <expand macro="element_assert" name="bcftools_stats" columns="28" lines="2" text="Test1"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1258 <expand macro="element_assert" name="busco" columns="8" lines="2" text="busco_txt"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1259 <expand macro="element_assert" name="featureCounts" columns="14" lines="7" text="5: TopHat on data 1, data 14, and data 13"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1260 <expand macro="element_assert" name="gatk_varianteval" columns="12" lines="2" text="gatk_varianteval_txt"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1261 <expand macro="element_assert" name="general_stats" columns="44" lines="23" text="x_bam"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1262 <expand macro="element_assert" name="htseq" columns="9" lines="2" text="htseq_txt"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1263 <expand macro="element_assert" name="picard_AlignmentSummaryMetrics" columns="26" lines="2" text="D11_H4K16ac_Rep1_R1_fastq_gz"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1264 <expand macro="element_assert" name="picard_RnaSeqMetrics" columns="27" lines="2" text="picard_CollectRnaSeqMetrics_bam"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1265 <expand macro="element_assert" name="picard_baseContent" columns="11" lines="2" text="D11_H4K16ac_Rep1_R1_fastq_gz"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1266 <expand macro="element_assert" name="picard_dups" columns="10" lines="2" text="dataset_114"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1267 <expand macro="element_assert" name="picard_insertSize" columns="23" lines="2" text="dataset_197_FR"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1268 <expand macro="element_assert" name="prokka" columns="11" lines="3" text="Sample2"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1269 <expand macro="element_assert" name="qualimap_bamqc_genome_results" columns="12" lines="2" text="x_bam"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1270 <expand macro="element_assert" name="quast" columns="50" lines="2" text="14892_1#15"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1271 <expand macro="element_assert" name="samblaster" columns="5" lines="2" text="virtual-normal"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1272 <expand macro="element_assert" name="samtools_flagstat" columns="34" lines="2" text="samtools_flagstat_txt">
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1273 <has_text text="samtools_flagstat" />
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1274 <has_text text="mapped_passed" />
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1275 <has_text text="20689039" />
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1276 </expand>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1277 <expand macro="element_assert" name="samtools_idxstats" columns="68" lines="2" text="samtools_idxstats_txt_idxstat"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1278 <expand macro="element_assert" name="samtools_stats" columns="40" lines="2" text="samtools_stats_txt"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1279 <expand macro="element_assert" name="snpeff" columns="169" lines="2" text="snpeff_csv"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1280 <expand macro="element_assert" name="sources" columns="4" lines="33" text="Bamtools"/>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1281 </output_collection>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1282 </test>
18 c19b16e5729c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9" iuc parents: 17 diff changeset	1283 <test expect_num_outputs="2">
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1284 <repeat name="results">
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1285 <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	1286 <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	1287 <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	1288 <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	1289 <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	1290 <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	1291 <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	1292 <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	1293 <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	1294 <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	1295 </conditional>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1296 </repeat>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1297 <output name="html_report" file="report_manual_custom_content.html" compare="sim_size"/>
18 c19b16e5729c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9" iuc parents: 17 diff changeset	1298 <output_collection name="stats" type="list" count="1"/>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1299 </test>
18 c19b16e5729c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9" iuc parents: 17 diff changeset	1300 <test expect_num_outputs="3">
15 3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1301 <repeat name="results">
3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1302 <conditional name="software_cond">
3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1303 <param name="software" value="fastqc" />
3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1304 <repeat name="output">
3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1305 <param name="type" value="data"/>
3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1306 <param name="input" value="fastqc_1.txt,fastqc_2.txt"/>
3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1307 </repeat>
3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1308 </conditional>
3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1309 </repeat>
3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1310 <param name="title" value="Title of the report"/>
3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1311 <param name="comment" value="Commment for the report"/>
18 c19b16e5729c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9" iuc parents: 17 diff changeset	1312 <param name="flat" value="true"/>
19 f7985e0479b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b" iuc parents: 18 diff changeset	1313 <param name="export" value="true"/>
15 3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1314 <output name="html_report">
3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1315 <assert_contents>
3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1316 <has_text text="Title of the report" />
3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1317 <has_text text="Commment for the report" />
3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1318 <has_text text="fastqc_seq_heatmap_key_t" />
3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1319 </assert_contents>
3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1320 </output>
20 c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1321 <output_collection name="stats" type="list" count="3">
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1322 <expand macro="element_assert" name="fastqc" columns="22" lines="3" text="poulet5_2"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1323 <expand macro="element_assert" name="general_stats" columns="6" lines="3" text="poulet5_2"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1324 <expand macro="element_assert" name="sources" columns="4" lines="3" text="FastQC"/>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1325 </output_collection>
c1a4b5f3b432 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" iuc parents: 19 diff changeset	1326 <output_collection name="plots" type="list" count="7">
15 3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1327 <element name="fastqc_per_base_sequence_quality_plot_1" file="mqc_fastqc_per_base_sequence_quality_plot_1.txt" compare="sim_size" delta="10"/>
3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1328 </output_collection>
3d93dd18d9f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" iuc parents: 13 diff changeset	1329 </test>
21 75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1330 <test expect_num_outputs="2">
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1331 <repeat name="results">
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1332 <conditional name="software_cond">
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1333 <param name="software" value="pycoqc" />
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1334 <param name="input" value="pycoqc.json"/>
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1335 </conditional>
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1336 </repeat>
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1337 <param name="title" value="Title of the report"/>
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1338 <param name="comment" value="Commment for the report"/>
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1339 <!-- <param name="flat" value="true"/> -->
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1340 <output name="html_report">
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1341 <assert_contents>
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1342 <has_text text="Title of the report" />
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1343 <has_text text="Commment for the report" />
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1344 <has_text text="General Statistics" />
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1345 <has_text text="pycoqc_count_plot" />
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1346 <has_text text="pycoqc_read_len_plot" />
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1347 <has_text text="pycoqc_read_qual_plot" />
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1348 </assert_contents>
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1349 </output>
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1350 <output_collection name="stats" type="list" count="2"/>
75c93c70d094 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" iuc parents: 20 diff changeset	1351 </test>
0 3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1352 </tests>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1353 <help><![CDATA[
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1354 What it does
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1355
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1356 `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	1357
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1358 Inputs
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1359
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1360 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	1361
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1362 ----
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1363
17 5e33b465d8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc" iuc parents: 16 diff changeset	1364 The first integration of this tool was made by
5e33b465d8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc" iuc parents: 16 diff changeset	1365 `@cmonjeau <https://github.com/cmonjeau>`_ and `@yvanlebras <https://github.com/yvanlebras>`_.
5e33b465d8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc" iuc parents: 16 diff changeset	1366 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	1367 ]]></help>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1368 <citations>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1369 <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	1370 </citations>
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 iuc parents: diff changeset	1371 </tool>

Mercurial > repos > iuc > multiqc

annotate multiqc.xml @ 21:75c93c70d094 draft