multiqc: macros.xml annotate

annotate macros.xml @ 23:abfd8a6544d7 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a

author	iuc
date	Sat, 10 Dec 2022 11:22:18 +0000
parents	9a913cdee30e
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>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	2 <token name="@TOOL_VERSION@">1.11</token>
23 abfd8a6544d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a iuc parents: 22 diff changeset	3 <token name="@VERSION_SUFFIX@">1</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>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	12 </requirements>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	13 </xml>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	14
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	15 <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	16 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	17 #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	18 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	19
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	20 <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	21 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	22 #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	23 #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	24 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	25 #set $file_paths += [$file_path]
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	26 grep -q '$pattern' $file \|\| die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	27 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	28 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	29
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	30 <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	31 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	32 #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	33 mkdir '$repeat_dir' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	34 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	35
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	36 <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	37 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	38 #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	39 mkdir '$repeat_dir' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	40 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	41 <token name="@CREATE_REPEAT_DIR_2@">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	42 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	43 #set repeat_dir = os.path.join($software_dir, str($repeat2.type.type) + '_' + str($j))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	44 mkdir '$repeat_dir' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	45 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	46 <token name="@LN_FILES@">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	47 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	48 #set file_paths = []
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	49 #for $file in $repeat.software_cond.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	50 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	51 #set file_path = os.path.join($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	52 @CHECK_LN_FILE@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	53 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	54 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	55
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	56 <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	57 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	58 #set file_paths = []
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	59 @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	60 #for $file in $repeat2.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	61 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	62 #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	63 @CHECK_LN_FILE@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	64 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	65 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	66
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	67 <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	68 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	69 #set file_paths = []
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	70 #for $file in $repeat2.type.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	71 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	72 #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	73 @CHECK_LN_FILE@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	74 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	75 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	76
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	77 <token name="@BISMARK_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	78 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	79 @CREATE_REPEAT_DIR_1@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	80 #if str($repeat2.type) == "align"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	81 #for $file in $repeat2.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	82 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	83 #set file_path = os.path.join($repeat_dir, str($identifier) + '_SE_report.txt')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	84 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	85 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	86 #elif str($repeat2.type) == "dedup"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	87 #for $file in $repeat2.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	88 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	89 #set file_path = os.path.join($repeat_dir, str($identifier) + '_deduplication_report.txt')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	90 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	91 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	92 #elif str($repeat2.type) == "meth_extract"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	93 #for $file in $repeat2.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	94 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	95 #set file_path = os.path.join($repeat_dir, str($identifier) + '_splitting_report.txt')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	96 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	97 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	98 #elif str($repeat2.type) == "m_bias"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	99 #for $file in $repeat2.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	100 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	101 #set file_path = os.path.join($repeat_dir, str($identifier) + '_M-bias.txt')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	102 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	103 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	104 #elif str($repeat2.type) == "bam2nuc"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	105 #for $file in $repeat2.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	106 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	107 #set file_path = os.path.join($repeat_dir, str($identifier) + '.nucleotide_stats.txt')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	108 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	109 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	110 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	111 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	112 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	113
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	114 <token name="@DEEPTOOLS_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	115 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	116 #if str($repeat2.type) == "bamPEFragmentSize"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	117 #set $pattern = "Frag."
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	118 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	119 #elif str($repeat2.type) == "estimateReadFiltering"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	120 #set $pattern = "Internally-determined Duplicate"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	121 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	122 #elif str($repeat2.type) == "plotCoverageStdout"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	123 #set $pattern = "sample"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	124 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	125 #elif str($repeat2.type) == "plotCoverageOutRawCounts"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	126 #set $pattern = "#plotCoverage --outRawCounts"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	127 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	128 #elif str($repeat2.type) == "plotEnrichment"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	129 #set $pattern = "featureReadCount"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	130 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	131 #elif str($repeat2.type) == "plotFingerprintOutRawCounts"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	132 #set $pattern = "#plotFingerprint --outRawCounts"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	133 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	134 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	135 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	136 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	137
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	138 <token name="@PICCARD_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	139 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	140 #if str($repeat2.type) == "alignment_metrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	141 #set $pattern = "picard.analysis.AlignmentSummaryMetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	142 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	143 #elif str($repeat2.type) == "basedistributionbycycle"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	144 #set $pattern = "picard.analysis.BaseDistributionByCycleMetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	145 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	146 #elif str($repeat2.type) == "gcbias"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	147 #set $pattern = "picard.analysis.GcBias"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	148 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	149 #elif str($repeat2.type) == "hsmetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	150 #set $pattern = "picard.analysis.directed.HsMetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	151 @ @
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	152 #elif str($repeat2.type) == "insertsize"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	153 #set $pattern = "picard.analysis.InsertSizeMetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	154 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	155 #elif str($repeat2.type) == "markdups"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	156 #set $pattern = "MarkDuplicates"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	157 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	158 #elif str($repeat2.type) == "oxogmetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	159 #set $pattern = "picard.analysis.CollectOxoGMetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	160 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	161 #elif str($repeat2.type) == "pcr_metrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	162 #set $pattern = "picard.analysis.directed.TargetedPcrMetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	163 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	164 #elif str($repeat2.type) == "rnaseqmetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	165 #set $pattern = "Collect"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	166 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	167 #elif str($repeat2.type) == "rrbs_metrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	168 #set $pattern = "picard.analysis.RrbsSummaryMetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	169 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	170 #elif str($repeat2.type) == "wgs_metrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	171 #set $pattern = "picard.analysis.CollectWgsMetrics$WgsMetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	172 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	173 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	174 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	175 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	176
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	177 <token name="@FASTQC_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	178 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	179 @CREATE_REPEAT_DIR_1@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	180 #if str($repeat2.type) == "data"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	181 #for $k, $file in enumerate($repeat2.input)
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	182 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	183 #set file_path = os.path.join($file_dir, 'fastqc_data.txt')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	184 mkdir '$file_dir' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	185 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	186 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	187 #elif str($repeat2.type) == "theoretical_gc"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	188 #for $file in $repeat2.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	189 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	190 #set file_path = os.path.join($repeat_dir, str($identifier) + '_fastqc_theoretical_gc')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	191 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	192 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	193 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	194 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	195 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	196
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	197 <token name="@RSEQ_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	198 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	199 @CREATE_REPEAT_DIR_2@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	200 #if str($repeat2.type.type) == "bam_stat"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	201 #set $pattern = "Proper-paired reads map to different chrom:"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	202 @LN_3_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	203 #elif str($repeat2.type.type) == "gene_body_coverage"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	204 #for $k, $file in enumerate($repeat2.type.input)
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	205 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.geneBodyCoverage.txt')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	206 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	207 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	208 #elif str($repeat2.type.type) == "inner_distance"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	209 #for $k, $file in enumerate($repeat2.type.input)
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	210 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.inner_distance_freq.txt')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	211 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	212 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	213 #elif str($repeat2.type.type) == "junction_annotation"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	214 #set $pattern = "Partial Novel Splicing Junctions:"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	215 @LN_3_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	216 #elif str($repeat2.type.type) == "read_gc"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	217 #for $k, $file in enumerate($repeat2.type.input)
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	218 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.GC.xls')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	219 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	220 #end for
23 abfd8a6544d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a iuc parents: 22 diff changeset	221 #elif str($repeat2.type.type) == "junction_saturation"
abfd8a6544d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a iuc parents: 22 diff changeset	222 #for $k, $file in enumerate($repeat2.type.input)
abfd8a6544d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a iuc parents: 22 diff changeset	223 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.junctionSaturation_plot.r')
abfd8a6544d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a iuc parents: 22 diff changeset	224 ln -s '${file}' '$file_path' &&
abfd8a6544d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a iuc parents: 22 diff changeset	225 #end for
22 9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	226 #elif str($repeat2.type.type) == "read_distribution"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	227 #set $pattern = "Group Total_bases Tag_count Tags/Kb"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	228 @LN_3_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	229 #elif str($repeat2.type.type) == "read_duplication_pos"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	230 #for $k, $file in enumerate($repeat2.type.input)
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	231 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.pos.DupRate.xls')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	232 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	233 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	234 #elif str($repeat2.type.type) == "infer_experiment"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	235 #set $pattern = "Fraction of reads explained by"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	236 #for $file in $repeat2.type.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	237 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	238 #set file_path = os.path.join($repeat_dir, str($identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	239 grep -q "$pattern" $file \|\| die "'$pattern' not found in the file" &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	240 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	241 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	242 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	243 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	244 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	245
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	246 <token name="@VCFTOOLS_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	247 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	248 @CREATE_REPEAT_DIR_2@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	249 #if str($repeat2.type.type) == "relatedness2"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	250 #for $file in $repeat2.type.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	251 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	252 #set file_path = os.path.join($repeat_dir, str($identifier) + '.relatedness2')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	253 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	254 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	255 #elif str($repeat2.type) == "tstv_by_count"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	256 #for $file in $repeat2.type.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	257 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	258 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.count')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	259 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	260 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	261 #elif str($repeat2.type) == "tstv_by_qual"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	262 #for $file in $repeat2.type.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	263 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	264 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.qual')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	265 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	266 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	267 #elif str($repeat2.type) == "tstv_summary"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	268 #for $file in $repeat2.type.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	269 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	270 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.summary')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	271 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	272 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	273 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	274 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	275 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	276
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	277 <token name="@QUALIMAP_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	278 #for $file in $repeat.software_cond.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	279 #if re.search("genome_results", str($file.element_identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	280 sample="\$(grep 'bam file = ' $file \| sed 's/bam file = //g' \| sed 's: ::g')" &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	281 dir_name="$software_dir/\${sample}" &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	282 mkdir -p \${dir_name} &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	283 filepath_1="\${dir_name}/genome_results.txt" &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	284 ln -sf '$file' \${filepath_1} &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	285 #elif re.search("coverage_histogram", str($file.element_identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	286 nested_dir_name="\${dir_name}/raw_data_qualimapReport/" &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	287 mkdir -p \${nested_dir_name} &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	288 filepath_2="\${nested_dir_name}/coverage_histogram.txt" &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	289 ln -sf '$file' \${filepath_2} &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	290 #elif re.search("gc-content_distribution", str($file.element_identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	291 nested_dir_name="\${dir_name}/raw_data_qualimapReport/" &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	292 mkdir -p \${nested_dir_name} &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	293 filepath_3="\${nested_dir_name}/mapped_reads_gc-content_distribution.txt" &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	294 ln -sf '$file' \${filepath_3} &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	295 #else
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	296 #pass
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	297 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	298 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	299 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	300
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	301 <token name="@SALMON_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	302 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	303 @CREATE_REPEAT_DIR_2@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	304 #if str($repeat2.type.type) == "meta"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	305 #for $k, $file in enumerate($repeat2.type.input)
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	306 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	307 #set file_path = os.path.join($file_dir, 'meta_info.json')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	308 mkdir '$file_dir' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	309 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	310 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	311 #elif str($repeat2.type.type) == "fld"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	312 #for $k, $file in enumerate($repeat2.type.input)
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	313 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	314 #set file_path = os.path.join($file_dir,'flenDist.txt')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	315 mkdir '$file_dir' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	316 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	317 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	318 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	319 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	320 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	321
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	322 <token name="@SAMTOOLS_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	323 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	324 @CREATE_REPEAT_DIR_2@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	325 #if str($repeat2.type.type) == "stats"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	326 #set $pattern = "This file was produced by samtools stats"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	327 @LN_3_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	328 #elif str($repeat2.type.type) == "flagstat"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	329 #set $pattern = "in total (QC-passed reads + QC-failed reads)"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	330 @LN_3_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	331 #elif str($repeat2.type.type) == "idxstats"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	332 #for $file in $repeat2.type.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	333 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	334 #set file_path = os.path.join($repeat_dir, str($identifier) + '_idxstat')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	335 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	336 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	337 #elif str($repeat2.type.type) == "rmdup"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	338 #set $pattern = "[bam_rmdup"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	339 @LN_3_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	340 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	341 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	342 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	343
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	344 <token name="@STAR_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	345 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	346 @CREATE_REPEAT_DIR_2@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	347 #if str($repeat2.type.type) == "log"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	348 #for $file in $repeat2.type.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	349 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	350 #set file_path = os.path.join($repeat_dir, str($identifier) + '_Log.final.out')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	351 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	352 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	353 #elif str($repeat2.type.type) == "genecounts"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	354 #for $file in $repeat2.type.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	355 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	356 #set file_path = os.path.join($repeat_dir, str($identifier) + '_ReadsPerGene.out.tab')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	357 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	358 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	359 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	360 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	361 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	362
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	363 <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	364 <element name="@NAME@">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	365 <assert_contents>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	366 <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	367 <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	368 <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	369 <yield/>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	370 </assert_contents>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	371 </element>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	372 </xml>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	373
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	374 <xml name="citations">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	375 <citations>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	376 <citation type="doi">10.1101/gr.244293.118</citation>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	377 </citations>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	378 </xml>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3" iuc parents: diff changeset	379 </macros>

Mercurial > repos > iuc > multiqc

annotate macros.xml @ 23:abfd8a6544d7 draft default tip