Mercurial > repos > iuc > macs2
comparison macs2_callpeak.xml @ 7:f5d67c722d67 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4583af716424e402e1f99e2181cfb954f565f681
| author | iuc |
|---|---|
| date | Wed, 12 Apr 2017 01:47:28 -0400 |
| parents | 2119d851a53b |
| children | e8a060164e11 |
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| 6:2119d851a53b | 7:f5d67c722d67 |
|---|---|
| 27 #end if | 27 #end if |
| 28 #end for | 28 #end for |
| 29 | 29 |
| 30 @effective_genome_size@ | 30 @effective_genome_size@ |
| 31 | 31 |
| 32 --bw '${$band_width}' | 32 --bw '${band_width}' |
| 33 @mfold_command@ | 33 @mfold_command@ |
| 34 | 34 |
| 35 ## advanced options | 35 ## advanced options |
| 36 #if $advanced_options.advanced_options_selector == "on": | 36 #if $advanced_options.advanced_options_selector == "on": |
| 37 $advanced_options.nolambda | 37 $advanced_options.nolambda |
| 72 #if $nomodel_type.nomodel_type_selector == "nomodel": | 72 #if $nomodel_type.nomodel_type_selector == "nomodel": |
| 73 --nomodel | 73 --nomodel |
| 74 --extsize '${ nomodel_type.extsize }' | 74 --extsize '${ nomodel_type.extsize }' |
| 75 #end if | 75 #end if |
| 76 | 76 |
| 77 2> $temp_stderr) | 77 2>&1 > $temp_stderr) |
| 78 #if "peaks_tabular" in str($outputs).split(','): | 78 #if "peaks_tabular" in str($outputs).split(','): |
| 79 && | 79 && |
| 80 cp MACS2_peaks.xls '${ output_tabular }' | 80 cp MACS2_peaks.xls '${ output_tabular }' |
| 81 #end if | 81 #end if |
| 82 | 82 |
| 93 count=`ls -1 MACS2* 2>/dev/null | wc -l`; | 93 count=`ls -1 MACS2* 2>/dev/null | wc -l`; |
| 94 if [ \$count != 0 ]; | 94 if [ \$count != 0 ]; |
| 95 then | 95 then |
| 96 mkdir '${ output_extra_files.files_path }' && | 96 mkdir '${ output_extra_files.files_path }' && |
| 97 cp MACS2* '${ output_extra_files.files_path }' && | 97 cp MACS2* '${ output_extra_files.files_path }' && |
| 98 python '$__tool_directory__/dir2html.py' | 98 python '$__tool_directory__/dir2html.py' |
| 99 '${ output_extra_files.files_path }' $temp_stderr > '${ output_extra_files }' | 99 '${ output_extra_files.files_path }' $temp_stderr > '${ output_extra_files }'; |
| 100 fi; | 100 fi; |
| 101 ) | 101 ) |
| 102 #end if | 102 #end if |
| 103 && | 103 && |
| 104 exit_code_for_galaxy=\$? && | 104 exit_code_for_galaxy=\$? && |
| 249 <param name="input_control_file" value="Control_200K.bed" ftype="bed"/> | 249 <param name="input_control_file" value="Control_200K.bed" ftype="bed"/> |
| 250 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/> | 250 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/> |
| 251 <param name="cutoff_options_selector" value="qvalue"/> | 251 <param name="cutoff_options_selector" value="qvalue"/> |
| 252 <param name="qvalue" value="0.05"/> | 252 <param name="qvalue" value="0.05"/> |
| 253 <param name="band_width" value="300"/> | 253 <param name="band_width" value="300"/> |
| 254 <param name="outputs" value="peaks_tabular,bdg"/> | 254 <param name="outputs" value="peaks_tabular,bdg,html"/> |
| 255 <param name="effective_genome_size_options_selector" value="user_defined" /> | 255 <param name="effective_genome_size_options_selector" value="user_defined" /> |
| 256 <param name="gsize" value="3300000000" /> | 256 <param name="gsize" value="3300000000" /> |
| 257 <param name="lower" value="5" /> | 257 <param name="lower" value="5" /> |
| 258 <param name="upper" value="50" /> | 258 <param name="upper" value="50" /> |
| 259 <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg" lines_diff="1"/> | 259 <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg" lines_diff="1"/> |
| 260 <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg" lines_diff="1"/> | 260 <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg" lines_diff="1"/> |
| 261 <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="1"/> | 261 <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="1"/> |
| 262 <output name="output_extra_files"> | |
| 263 <assert_contents> | |
| 264 <has_text text="Additional output created by MACS2" /> | |
| 265 </assert_contents> | |
| 266 </output> | |
| 267 | |
| 262 </test> | 268 </test> |
| 263 <test> | 269 <test> |
| 264 <param name="input_control_file" value="Control_200K.bed" ftype="bed"/> | 270 <param name="input_control_file" value="Control_200K.bed" ftype="bed"/> |
| 265 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/> | 271 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/> |
| 266 <param name="cutoff_options_selector" value="qvalue"/> | 272 <param name="cutoff_options_selector" value="qvalue"/> |