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comparison multiqc.xml @ 9:a531ae71d397 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 31d721c19f5681dfe542dd23185c06c8f29f1945
author iuc
date Wed, 25 Apr 2018 07:59:34 -0400
parents 6ef9e2d46af4
children b0ce3f403e30
comparison
equal deleted inserted replaced
8:6ef9e2d46af4 9:a531ae71d397
6 <![CDATA[ 6 <![CDATA[
7 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier)) 7 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
8 ]]></token> 8 ]]></token>
9 <token name="@CHECK_LN_FILE@"> 9 <token name="@CHECK_LN_FILE@">
10 <![CDATA[ 10 <![CDATA[
11 #if $file_path in $file_paths
12 #set $file_path += '_' + str($file_paths.count($file_path))
13 #end if
14 #set $file_paths += [$file_path]
11 grep -q "$pattern" $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" && 15 grep -q "$pattern" $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
12 ln -s '$file' '$file_path' && 16 ln -s '$file' '$file_path' &&
13 ]]></token> 17 ]]></token>
14 <token name="@CREATE_REPEAT_DIR_1@"> 18 <token name="@CREATE_REPEAT_DIR_1@">
15 <![CDATA[ 19 <![CDATA[
21 #set repeat_dir = os.path.join($software_dir, str($repeat2.type.type) + '_' + str($j)) 25 #set repeat_dir = os.path.join($software_dir, str($repeat2.type.type) + '_' + str($j))
22 mkdir '$repeat_dir' && 26 mkdir '$repeat_dir' &&
23 ]]></token> 27 ]]></token>
24 <token name="@LN_FILES@"> 28 <token name="@LN_FILES@">
25 <![CDATA[ 29 <![CDATA[
30 #set file_paths = []
26 #for $file in $repeat.software_cond.input 31 #for $file in $repeat.software_cond.input
27 @ESCAPE_IDENTIFIER@ 32 @ESCAPE_IDENTIFIER@
28 #set file_path = os.path.join($software_dir, str($identifier)) 33 #set file_path = os.path.join($software_dir, str($identifier))
29 @CHECK_LN_FILE@ 34 @CHECK_LN_FILE@
30 #end for 35 #end for
31 ]]></token> 36 ]]></token>
32 <token name="@LN_2_FILES@"> 37 <token name="@LN_2_FILES@">
33 <![CDATA[ 38 <![CDATA[
39 #set file_paths = []
34 @CREATE_REPEAT_DIR_1@ 40 @CREATE_REPEAT_DIR_1@
35 #for $file in $repeat2.input 41 #for $file in $repeat2.input
36 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier)) 42 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
37 #set file_path = os.path.join($repeat_dir, str($identifier)) 43 #set file_path = os.path.join($repeat_dir, str($identifier))
38 @CHECK_LN_FILE@ 44 @CHECK_LN_FILE@
39 #end for 45 #end for
40 ]]></token> 46 ]]></token>
41 <token name="@LN_3_FILES@"> 47 <token name="@LN_3_FILES@">
42 <![CDATA[ 48 <![CDATA[
49 #set file_paths = []
43 #for $file in $repeat2.type.input 50 #for $file in $repeat2.type.input
44 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier)) 51 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
45 #set file_path = os.path.join($repeat_dir, str($identifier)) 52 #set file_path = os.path.join($repeat_dir, str($identifier))
46 @CHECK_LN_FILE@ 53 @CHECK_LN_FILE@
47 #end for 54 #end for
866 </conditional> 873 </conditional>
867 </repeat> 874 </repeat>
868 <repeat name="results"> 875 <repeat name="results">
869 <conditional name="software_cond"> 876 <conditional name="software_cond">
870 <param name="software" value="hicexplorer" /> 877 <param name="software" value="hicexplorer" />
871 <param name="input" value="hicexplorer1.log,hicexplorer2.log" /> 878 <param name="input" value="hicexplorer1.log,hicexplorer1.log,hicexplorer2.log" />
872 </conditional> 879 </conditional>
873 </repeat> 880 </repeat>
874 <repeat name="results"> 881 <repeat name="results">
875 <conditional name="software_cond"> 882 <conditional name="software_cond">
876 <param name="software" value="kallisto" /> 883 <param name="software" value="kallisto" />
908 <has_text text="hisat2_se_plot" /> 915 <has_text text="hisat2_se_plot" />
909 <has_text text="kallisto_alignment" /> 916 <has_text text="kallisto_alignment" />
910 <has_text text="star_alignment_plot" /> 917 <has_text text="star_alignment_plot" />
911 <has_text text="tophat_alignment" /> 918 <has_text text="tophat_alignment" />
912 <has_text text="hicexplorer" /> 919 <has_text text="hicexplorer" />
913 920 <has_text text="hicexplorer1_log_1" />
914 </assert_contents> 921 </assert_contents>
915 </output> 922 </output>
916 <output_collection name="stats" type="list"> 923 <output_collection name="stats" type="list">
917 <element name="bismark_alignment" file="bismark_stats.tabular" compare="sim_size" delta="10"/> 924 <element name="bismark_alignment" file="bismark_stats.tabular" compare="sim_size" delta="10"/>
918 <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="20"/> 925 <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="20"/>