multiqc: macros.xml annotate

annotate macros.xml @ 30:26ee5e11ecbe draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4

author	iuc
date	Thu, 15 Jan 2026 20:39:44 +0000
parents	e4dd4c0622f6
children

rev	line source
22 9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	1 <macros>
30 26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4 iuc parents: 29 diff changeset	2 <token name="@TOOL_VERSION@">1.33</token>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4 iuc parents: 29 diff changeset	3 <token name="@VERSION_SUFFIX@">0</token>
22 9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	4 <xml name="bio_tools">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	5 <xrefs>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	6 <xref type="bio.tools">multiqc</xref>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	7 </xrefs>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	8 </xml>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	9 <xml name="requirements">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	10 <requirements>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	11 <requirement type="package" version="@TOOL_VERSION@">multiqc</requirement>
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	12 </requirements>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	13 </xml>
30 26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4 iuc parents: 29 diff changeset	14 <!--This stdio rule is temporary because of an issue with CheckM2 report columns, it needs to be removed when the issue is fixed -->
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4 iuc parents: 29 diff changeset	15 <xml name="stdio">
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4 iuc parents: 29 diff changeset	16 <stdio>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4 iuc parents: 29 diff changeset	17 <regex
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4 iuc parents: 29 diff changeset	18 match="Module 'checkm2: .not found in the file."
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4 iuc parents: 29 diff changeset	19 source="both"
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4 iuc parents: 29 diff changeset	20 level="fatal"
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4 iuc parents: 29 diff changeset	21 description="Invalid CheckM2 TSV file: required header not found" />
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4 iuc parents: 29 diff changeset	22 </stdio>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4 iuc parents: 29 diff changeset	23 </xml>
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	24 <xml name="citations">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	25 <citations>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	26 <citation type="doi">10.1101/gr.244293.118</citation>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	27 </citations>
22 9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	28 </xml>
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	29 <xml name="configfile">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	30 <configfiles>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	31 <configfile name="multiqc_config">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	32 <![CDATA[
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	33 custom_data:
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	34 #for $i, $repeat in enumerate( $results )
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	35 #if str($repeat.software_cond.software) == "custom_content"
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	36 section_$i:
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	37 file_format: 'tsv'
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	38 section_name: '$repeat.software_cond.section_name'
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	39 title: '$repeat.software_cond.title'
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	40 description: '$repeat.software_cond.description'
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	41 plot_type: '$repeat.software_cond.plot_type'
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	42 pconfig:
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	43 id: 'section_${i}_${repeat.software_cond.plot_type}'
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	44 ylab: '$repeat.software_cond.ylab'
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	45 xlab: '$repeat.software_cond.xlab'
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	46 #end if
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	47 #end for
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	48 sp:
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	49 #for $i, $repeat in enumerate( $results )
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	50 #if str($repeat.software_cond.software) == "custom_content"
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	51 section_$i:
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	52 fn: 'file_${i}_*'
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	53 #end if
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	54 #end for
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	55 ]]></configfile>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	56 </configfiles>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	57 </xml>
22 9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	58 <token name="@ESCAPE_IDENTIFIER@">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	59 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	60 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	61 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	62 <token name="@CHECK_LN_FILE@">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	63 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	64 #if $file_path in $file_paths
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	65 #set $file_path += '_' + str($file_paths.count($file_path))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	66 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	67 #set $file_paths += [$file_path]
27 7591bce96601 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee iuc parents: 26 diff changeset	68 grep -Pq '$pattern' $file \|\| die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
22 9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	69 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	70 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	71 <token name="@CREATE_REPEAT_DIR_1@">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	72 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	73 #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	74 mkdir '$repeat_dir' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	75 ]]></token>
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	76 <token name="@CREATE_REPEAT_DIR_2@">
22 9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	77 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	78 #set repeat_dir = os.path.join($software_dir, str($repeat2.type.type) + '_' + str($j))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	79 mkdir '$repeat_dir' &&
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	80 ]]></token>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	81 <token name="@LN_FILES@">
22 9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	82 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	83 #set file_paths = []
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	84 #for $file in $repeat.software_cond.input:
22 9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	85 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	86 #set file_path = os.path.join($software_dir, str($identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	87 @CHECK_LN_FILE@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	88 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	89 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	90 <token name="@LN_2_FILES@">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	91 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	92 #set file_paths = []
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	93 @CREATE_REPEAT_DIR_1@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	94 #for $file in $repeat2.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	95 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	96 #set file_path = os.path.join($repeat_dir, str($identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	97 @CHECK_LN_FILE@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	98 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	99 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	100 <token name="@LN_3_FILES@">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	101 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	102 #set file_paths = []
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	103 #for $file in $repeat2.type.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	104 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	105 #set file_path = os.path.join($repeat_dir, str($identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	106 @CHECK_LN_FILE@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	107 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	108 ]]></token>
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	109 <!-- is currently not used -->
22 9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	110 <xml name="element_assert" token_name="" token_lines="" token_columns="" token_text="">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	111 <element name="@NAME@">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	112 <assert_contents>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	113 <has_n_columns n="@COLUMNS@"/>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	114 <has_n_lines n="@LINES@"/>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	115 <has_text text="@TEXT@"/>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	116 <yield/>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	117 </assert_contents>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	118 </element>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	119 </xml>
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	120 <xml name="general_tests">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	121 <!--Test 01-->
29 e4dd4c0622f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4095773348da6faeb6096f58785b66898b09befa iuc parents: 28 diff changeset	122 <test expect_num_outputs="4">
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	123 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	124 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	125 <param name="software" value="cutadapt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	126 <param name="input" value="cutadapt.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	127 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	128 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	129 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	130 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	131 <param name="software" value="fastp"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	132 <param name="input" value="fastp1.json.txt,fastp2.json.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	133 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	134 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	135 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	136 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	137 <param name="software" value="fastqc"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	138 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	139 <param name="type" value="data"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	140 <param name="input" value="fastqc_1.txt,fastqc_2.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	141 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	142 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	143 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	144 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	145 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	146 <param name="software" value="flexbar"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	147 <param name="input" value="flexbar.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	148 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	149 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	150 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	151 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	152 <param name="software" value="slamdunk"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	153 <param name="input" value="slamdunk_summary.txt,slamdunk_reads1_overallrates.csv,slamdunk_reads2_overallrates.csv"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	154 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	155 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	156 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	157 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	158 <param name="software" value="sortmerna"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	159 <param name="input" value="sortmerna.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	160 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	161 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	162 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	163 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	164 <param name="software" value="trimmomatic"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	165 <param name="input" value="trimmomatic.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	166 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	167 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	168 <param name="title" value="Title of the report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	169 <param name="comment" value="Commment for the report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	170 <param name="flat" value="true"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	171 <param name="export" value="true"/>
29 e4dd4c0622f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4095773348da6faeb6096f58785b66898b09befa iuc parents: 28 diff changeset	172 <param name="png_plots" value="true"/>
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	173 <output name="html_report">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	174 <assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	175 <has_text text="Title of the report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	176 <has_text text="Commment for the report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	177 <has_text text="cutadapt_trimmed_sequences_plot"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	178 <has_text text="All-in-one FASTQ preprocessor"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	179 <has_text text="fastqc_seq_heatmap_key_t"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	180 <has_text text="flexbar_plot"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	181 <has_text text="Slamdunk"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	182 <has_text text="sortmerna-detailed-plot"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	183 <has_text text="trimmomatic_plot"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	184 </assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	185 </output>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	186 <output name="stats">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	187 <assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	188 <has_text text="dataset_33"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	189 <has_text text="R1_fq"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	190 <has_text text="poulet5_1"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	191 <has_text text="result_right"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	192 <has_text text="bwa-mem-fastq1_fq"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	193 <has_text text="25839_merged"/>
25 a7e081ceb76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 1805997f0c29291dd6fc96add4481422e28e6265 iuc parents: 24 diff changeset	194 <has_text text="slamdunk-retained"/>
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	195 <has_text text="C2"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	196 <has_n_lines n="11"/>
30 26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4 iuc parents: 29 diff changeset	197 <has_n_columns n="24"/>
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	198 </assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	199 </output>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	200 <output_collection name="plots" type="list" count="29"/>
30 26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4 iuc parents: 29 diff changeset	201 <output_collection name="png_plot" type="list" count="36"/>
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	202 </test>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	203 <!--Test 02-->
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	204 <test expect_num_outputs="2">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	205 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	206 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	207 <param name="software" value="bismark"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	208 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	209 <param name="type" value="align"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	210 <param name="input" value="bismark.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	211 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	212 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	213 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	214 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	215 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	216 <param name="software" value="bowtie2"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	217 <param name="input" value="bowtie2_1.txt,bowtie2_2.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	218 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	219 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	220 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	221 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	222 <param name="software" value="hisat2"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	223 <param name="input" value="hisat2_1.txt,hisat2_2.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	224 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	225 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	226 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	227 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	228 <param name="software" value="hicexplorer"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	229 <param name="input" value="hicexplorer1.log,hicexplorer1.log,hicexplorer2.log"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	230 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	231 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	232 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	233 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	234 <param name="software" value="kallisto"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	235 <param name="input" value="kallisto_1.txt,kallisto_2.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	236 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	237 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	238 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	239 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	240 <param name="software" value="macs2"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	241 <param name="input" value="macs_1.txt,macs_2.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	242 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	243 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	244 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	245 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	246 <param name="software" value="star"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	247 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	248 <conditional name="type">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	249 <param name="type" value="log"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	250 <param name="input" value="star_log.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	251 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	252 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	253 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	254 <conditional name="type">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	255 <param name="type" value="genecounts"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	256 <param name="input" value="star_counts.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	257 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	258 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	259 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	260 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	261 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	262 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	263 <param name="software" value="tophat"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	264 <param name="input" value="tophat.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	265 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	266 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	267 <output name="html_report">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	268 <assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	269 <has_text text="bismark-alignment"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	270 <has_text text="bowtie2_se_plot"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	271 <has_text text="mqc-module-section-bowtie2"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	272 <has_text text="hisat2_se_plot"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	273 <has_text text="MACS2"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	274 <has_text text="star_alignment_plot"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	275 <has_text text="tophat_alignment"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	276 <has_text text="hicexplorer"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	277 <has_text text="hicexplorer1_log_1"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	278 </assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	279 </output>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	280 <output name="stats">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	281 <assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	282 <has_text text="bismark_txt_SE_report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	283 <has_text text="bowtie2_1_txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	284 <has_text text="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	285 <has_text text="treat2"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	286 <has_text text="hicexplorer_3_hicexplorer2_log_small_test_rf"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	287 <has_text text="hisat2_2_txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	288 <has_text text="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	289 <has_text text="treat2"/>
25 a7e081ceb76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 1805997f0c29291dd6fc96add4481422e28e6265 iuc parents: 24 diff changeset	290 <has_text text="cutadapt-percent_trimmed"/>
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	291 <has_text text="star_log_txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	292 <has_text text="tophat_txtalign"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	293 <has_n_lines n="17"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	294 <has_n_columns n="23"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	295 </assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	296 </output>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	297 </test>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	298 <!--Test 03-->
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	299 <test expect_num_outputs="2">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	300 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	301 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	302 <param name="software" value="bamtools"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	303 <param name="input" value="bamtools.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	304 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	305 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	306 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	307 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	308 <param name="software" value="bcftools"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	309 <param name="input" value="bcftools.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	310 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	311 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	312 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	313 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	314 <param name="software" value="busco"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	315 <param name="input" value="busco.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	316 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	317 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	318 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	319 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	320 <param name="software" value="deeptools"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	321 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	322 <param name="type" value="bamPEFragmentSize"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	323 <param name="input" value="deeptools_bamPEFragmentSize.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	324 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	325 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	326 <param name="type" value="estimateReadFiltering"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	327 <param name="input" value="deeptools_estimateReadFiltering.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	328 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	329 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	330 <param name="type" value="plotCoverageStdout"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	331 <param name="input" value="deeptools_plotCoverageStdout.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	332 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	333 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	334 <param name="type" value="plotCoverageOutRawCounts"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	335 <param name="input" value="deeptools_plotCoverageOutRawCounts.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	336 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	337 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	338 <param name="type" value="plotEnrichment"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	339 <param name="input" value="deeptools_plotEnrichment.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	340 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	341 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	342 <param name="type" value="plotFingerprintOutRawCounts"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	343 <param name="input" value="deeptools_plotFingerprintOutRawCounts.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	344 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	345 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	346 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	347 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	348 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	349 <param name="software" value="featureCounts"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	350 <param name="input" value="featureCounts.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	351 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	352 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	353 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	354 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	355 <param name="software" value="gatk"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	356 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	357 <param name="type" value="base_recalibrator"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	358 <param name="input" value="gatk_BaseRecalibrator.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	359 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	360 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	361 <param name="type" value="varianteval"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	362 <param name="input" value="gatk_varianteval.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	363 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	364 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	365 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	366 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	367 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	368 <param name="software" value="htseq"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	369 <param name="input" value="htseq.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	370 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	371 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	372 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	373 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	374 <param name="software" value="picard"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	375 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	376 <param name="type" value="gcbias"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	377 <param name="input" value="picard_collectGcBias.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	378 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	379 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	380 <param name="type" value="insertsize"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	381 <param name="input" value="picard_CollectInsertSizeMetrics.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	382 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	383 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	384 <param name="type" value="markdups"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	385 <param name="input" value="picard_MarkDuplicates.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	386 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	387 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	388 <param name="type" value="basedistributionbycycle"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	389 <param name="input" value="picard_CollectBaseDistributionByCycle.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	390 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	391 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	392 <param name="type" value="rnaseqmetrics"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	393 <param name="input" value="picard_CollectRnaSeqMetrics.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	394 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	395 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	396 <param name="type" value="alignment_metrics"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	397 <param name="input" value="picard_CollectAlignmentSummaryMetrics.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	398 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	399 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	400 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	401 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	402 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	403 <param name="software" value="prokka"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	404 <param name="input" value="prokka_1.txt,prokka_2.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	405 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	406 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	407 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	408 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	409 <param name="software" value="qualimap"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	410 <param name="input" value="genome_results.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	411 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	412 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	413 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	414 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	415 <param name="software" value="quast"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	416 <param name="input" value="quast.tsv"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	417 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	418 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	419 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	420 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	421 <param name="software" value="rseqc"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	422 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	423 <conditional name="type">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	424 <param name="type" value="read_gc"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	425 <param name="input" value="rseqc.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	426 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	427 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	428 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	429 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	430 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	431 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	432 <param name="software" value="samblaster"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	433 <param name="input" value="samblaster.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	434 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	435 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	436 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	437 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	438 <param name="software" value="samtools"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	439 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	440 <conditional name="type">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	441 <param name="type" value="stats"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	442 <param name="input" value="samtools_stats.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	443 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	444 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	445 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	446 <conditional name="type">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	447 <param name="type" value="flagstat"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	448 <param name="input" value="samtools_flagstat.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	449 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	450 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	451 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	452 <conditional name="type">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	453 <param name="type" value="idxstats"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	454 <param name="input" value="samtools_idxstats.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	455 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	456 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	457 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	458 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	459 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	460 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	461 <param name="software" value="snpeff"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	462 <param name="input" value="snpeff.csv" ftype="csv"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	463 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	464 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	465 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	466 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	467 <param name="software" value="vcftools"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	468 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	469 <conditional name="type">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	470 <param name="type" value="tstv_by_qual"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	471 <param name="input" value="vcftools.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	472 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	473 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	474 <param name="input" value="vcftools.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	475 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	476 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	477 <output name="html_report">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	478 <assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	479 <has_text text="bamtools-stats"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	480 <has_text text="bcftools_stats_indel-lengths"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	481 <has_text text="busco-lineage-fungi_odb9"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	482 <has_text text="deeptools"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	483 <has_text text="featureCounts_assignment_plot"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	484 <has_text text="gatk_varianteval_variant_plot"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	485 <has_text text="htseq_assignment_plot"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	486 <has_text text="picard_alignment_readlength"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	487 <has_text text="picard-rna-assignment"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	488 <has_text text="picard-markduplicates"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	489 <has_text text="picard-insertsize"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	490 <has_text text="picard-gcbias"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	491 <has_text text="prokka_plot"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	492 <has_text text="qualimap"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	493 <has_text text="samblaster_duplicates"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	494 <has_text text="quast-stats"/>
30 26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4 iuc parents: 29 diff changeset	495 <has_text text="samtools-flagstat-pct"/>
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	496 <has_text text="snpeff"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	497 </assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	498 </output>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	499 <output name="stats">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	500 <assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	501 <has_text text="bamtools_txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	502 <has_text text="Test1"/>
25 a7e081ceb76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 1805997f0c29291dd6fc96add4481422e28e6265 iuc parents: 24 diff changeset	503 <has_text text="prokka-contigs"/>
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	504 <has_text text="5: TopHat on data 1, data 14, and data 13"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	505 <has_text text="gatk_varianteval_txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	506 <has_text text="x_bam"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	507 <has_text text="htseq_txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	508 <has_text text="picard_CollectRnaSeqMetrics_bam"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	509 <has_text text="dataset_114"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	510 <has_text text="Helicobacter pylori"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	511 <has_text text="Sample2"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	512 <has_text text="14892_1#15"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	513 <has_text text="samtools_flagstat_txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	514 <has_text text="mapped_passed"/>
25 a7e081ceb76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 1805997f0c29291dd6fc96add4481422e28e6265 iuc parents: 24 diff changeset	515 <has_text text="samtools_stats-error_rate"/>
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	516 <has_text text="samtools_stats_txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	517 <has_text text="snpeff_csv"/>
25 a7e081ceb76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 1805997f0c29291dd6fc96add4481422e28e6265 iuc parents: 24 diff changeset	518 <has_text text="bamtools-mapped_reads_pct"/>
a7e081ceb76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 1805997f0c29291dd6fc96add4481422e28e6265 iuc parents: 24 diff changeset	519 <has_text text="bamtools-duplicates_pct"/>
30 26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4 iuc parents: 29 diff changeset	520 <has_n_lines n="23"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4 iuc parents: 29 diff changeset	521 <has_n_columns n="55"/>
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	522 </assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	523 </output>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	524 </test>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	525 <!--Test 04-->
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	526 <test expect_num_outputs="2">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	527 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	528 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	529 <param name="software" value="custom_content"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	530 <param name="cc_select" value="manual"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	531 <param name="plot_type" value="linegraph"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	532 <param name="section_name" value="BPC"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	533 <param name="description" value="Sum of intensity (Y) of the most intense peaks at each retention time(X)"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	534 <param name="xlab" value="Retention Time"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	535 <param name="ylab" value="Base Peak Intensity"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	536 <param name="input" value="cc_ko15.bpc.tab,cc_wt15.bpc.tab"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	537 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	538 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	539 <output name="html_report" ftype="html">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	540 <assert_contents>
30 26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4 iuc parents: 29 diff changeset	541 <has_size value="2142211" delta="500"/>
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	542 </assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	543 </output>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	544 <!--output name="stats" ftype="tabular">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	545 Not created anymore. Proper test needed.
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	546 <assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	547 <has_n_lines n="2" />
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	548 </assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	549 </output-->
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	550 </test>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	551 <!--Test 05-->
29 e4dd4c0622f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4095773348da6faeb6096f58785b66898b09befa iuc parents: 28 diff changeset	552 <test expect_num_outputs="4">
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	553 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	554 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	555 <param name="software" value="fastqc"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	556 <repeat name="output">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	557 <param name="type" value="data"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	558 <param name="input" value="fastqc_1.txt,fastqc_2.txt"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	559 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	560 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	561 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	562 <param name="title" value="Title of the report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	563 <param name="comment" value="Commment for the report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	564 <param name="flat" value="true"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	565 <param name="export" value="true"/>
29 e4dd4c0622f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4095773348da6faeb6096f58785b66898b09befa iuc parents: 28 diff changeset	566 <param name="png_plots" value="true"/>
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	567 <output name="html_report">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	568 <assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	569 <has_text text="Title of the report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	570 <has_text text="Commment for the report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	571 <has_text text="fastqc_seq_heatmap_key_t"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	572 </assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	573 </output>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	574 <output name="stats" ftype="tabular">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	575 <assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	576 <has_text text="poulet5_2"/>
25 a7e081ceb76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 1805997f0c29291dd6fc96add4481422e28e6265 iuc parents: 24 diff changeset	577 <has_text text="fastqc-percent_gc"/>
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	578 <has_n_lines n="3"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	579 <has_n_columns n="7"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	580 </assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	581 </output>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	582 <output_collection name="plots" type="list" count="7">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	583 <element name="fastqc_per_base_sequence_quality_plot" file="mqc_fastqc_per_base_sequence_quality_plot_1.txt">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	584 <assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	585 <has_size size="2877" delta="200"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	586 </assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	587 </element>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	588 </output_collection>
30 26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4 iuc parents: 29 diff changeset	589 <output_collection name="png_plot" type="list" count="9"/>
29 e4dd4c0622f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4095773348da6faeb6096f58785b66898b09befa iuc parents: 28 diff changeset	590
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	591 </test>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	592 <!--Test 06-->
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	593 <test expect_num_outputs="2">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	594 <repeat name="results">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	595 <conditional name="software_cond">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	596 <param name="software" value="pycoqc"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	597 <param name="input" value="pycoqc.json"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	598 </conditional>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	599 </repeat>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	600 <param name="title" value="Title of the report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	601 <param name="comment" value="Commment for the report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	602 <!-- <param name="flat" value="true"/> -->
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	603 <output name="html_report">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	604 <assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	605 <has_text text="Title of the report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	606 <has_text text="Commment for the report"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	607 <has_text text="General Statistics"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	608 <has_text text="pycoqc_count_plot"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	609 <has_text text="pycoqc_read_len_plot"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	610 <has_text text="pycoqc_read_qual_plot"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	611 </assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	612 </output>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	613 <output name="stats" ftype="tabular">
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	614 <assert_contents>
25 a7e081ceb76a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 1805997f0c29291dd6fc96add4481422e28e6265 iuc parents: 24 diff changeset	615 <has_text text="pycoqc-passed_median_read_length"/>
24 f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	616 <has_text text="pycoqc_json"/>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	617 </assert_contents>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	618 </output>
f7e2f1eb3a16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58 iuc parents: 23 diff changeset	619 </test>
22 9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	620 </xml>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	621 </macros>

Mercurial > repos > iuc > multiqc

annotate macros.xml @ 30:26ee5e11ecbe draft default tip