Mercurial > repos > iuc > multiqc
comparison multiqc.xml @ 9:df99138d2776 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 31d721c19f5681dfe542dd23185c06c8f29f1945
| author | iuc |
|---|---|
| date | Wed, 25 Apr 2018 07:59:52 -0400 |
| parents | e0f4a651c6b9 |
| children | ce0f144f4835 |
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| 8:e0f4a651c6b9 | 9:df99138d2776 |
|---|---|
| 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"/> |