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comparison macs21_wrapper.xml @ 2:15889783e759 draft

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Fix bugs in tool operation and update dependencies.
author pjbriggs
date Thu, 12 Feb 2015 08:29:07 -0500
parents d0986d2be693
children a881c5b7162c
comparison
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1:d0986d2be693 2:15889783e759
1 <tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-1"> 1 <tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-2">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="2.7">python</requirement> 3 <requirement type="package" version="2.7">python</requirement>
4 <requirement type="package" version="1.8.1">numpy</requirement> 4 <requirement type="package" version="1.9">numpy</requirement>
5 <requirement type="package" version="2.1.0.20140616">macs2</requirement> 5 <requirement type="package" version="2.1.0.20140616">macs2</requirement>
6 </requirements> 6 </requirements>
7 <description>Model-based Analysis of ChIP-Seq</description> 7 <description>Model-based Analysis of ChIP-Seq</description>
8 <command interpreter="python"> 8 <command interpreter="python">
9 macs21_wrapper.py 9 macs21_wrapper.py
47 --qvalue=$major_command.pq_options.qvalue 47 --qvalue=$major_command.pq_options.qvalue
48 #else 48 #else
49 --pvalue=$major_command.pq_options.pvalue 49 --pvalue=$major_command.pq_options.pvalue
50 #end if 50 #end if
51 ## 51 ##
52 ## Bedgraph options
53 #if $major_command.bdg_options.bdg == True
54 -B $major_command.bdg_options.spmr
55 #end if
56 ##
52 ## Advanced options 57 ## Advanced options
53 #if str($major_command.advanced_options.advanced_options_selector) == 'on' 58 #if str($major_command.advanced_options.advanced_options_selector) == 'on'
54 --mfold $major_command.advanced_options.mfoldlo $major_command.advanced_options.mfoldhi 59 --mfold $major_command.advanced_options.mfoldlo $major_command.advanced_options.mfoldhi
55 $major_command.advanced_options.nolambda 60 $major_command.advanced_options.nolambda
56 #if $major_command.bdg_options.bdg == True
57 -B $major_command.bdg_options.spmr
58 #end if
59 $major_command.advanced_options.call_summits 61 $major_command.advanced_options.call_summits
60 #if str($major_command.advanced_options.keep_duplicates.keep_dup) == '' 62 #if str($major_command.advanced_options.keep_duplicates.keep_dup) == ''
61 --keep-dup $major_command.advanced_options.keep_duplicates.maximum_tags 63 --keep-dup $major_command.advanced_options.keep_duplicates.maximum_tags
62 #else 64 #else
63 --keep-dup $major_command.advanced_options.keep_duplicates.keep_dup 65 --keep-dup $major_command.advanced_options.keep_duplicates.keep_dup
64 #end if 66 #end if
65 #else 67 #else
66 ## Defaults if advanced options not set 68 ## Defaults if advanced options not set
67 --mfold 5 50 --keep-dup 1 69 --mfold 10 30 --keep-dup 1
68 #end if 70 #end if
69 ## 71 ##
70 ## Output files 72 ## Output files
71 --output-summits=$output_summits_bed_file 73 --output-summits=$output_summits_bed_file
72 --output-extra-files=$output_extra_files 74 --output-extra-files=$output_extra_files
80 --output-narrowpeaks=$output_narrowpeaks_file 82 --output-narrowpeaks=$output_narrowpeaks_file
81 #end if 83 #end if
82 ## 84 ##
83 ## Bedgraph outputs 85 ## Bedgraph outputs
84 #if str($major_command.bdg_options.bdg) == 'True' 86 #if str($major_command.bdg_options.bdg) == 'True'
85 --output-pileup $output_treat_pileup_file 87 --output-pileup=$output_treat_pileup_file
86 --output-lambda-bedgraph=$output_lambda_bedgraph_file 88 --output-lambda-bedgraph=$output_lambda_bedgraph_file
89 #if str($major_command.bdg_options.make_bigwig) == 'True'
90 --output-bigwig=$output_bigwig_file
91 --length=$GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${major_command.input_chipseq_file1.dbkey}.len
92 #end if
87 #end if 93 #end if
88 ## 94 ##
89 ## XLS/interval output 95 ## XLS/interval output
90 #if str($major_command.xls_to_interval) == 'True' 96 #if str($major_command.xls_to_interval) == 'True'
91 --output-xls-to-interval=$output_xls_to_interval_peaks_file 97 --output-xls-to-interval=$output_xls_to_interval_peaks_file
151 type="boolean" truevalue="True" falsevalue="False" checked="True" 157 type="boolean" truevalue="True" falsevalue="False" checked="True"
152 help="MACS2 XLS file will be output to the history in 'interval' format (suitable for subsequent analysis in Galaxy). Note that start positions are 1-based."/> 158 help="MACS2 XLS file will be output to the history in 'interval' format (suitable for subsequent analysis in Galaxy). Note that start positions are 1-based."/>
153 159
154 <conditional name="bdg_options"> 160 <conditional name="bdg_options">
155 <param name="bdg" 161 <param name="bdg"
156 label="Save fragment pileup, control lambda, -log10pvalue/qvalue in bedGraph" 162 label="Save treatment and control lambda pileups in bedGraph"
157 type="boolean" truevalue="-B" falsevalue="" checked="False" /> 163 type="boolean" truevalue="-B" falsevalue="" checked="False" />
158 <when value="-B"> 164 <when value="-B">
159 <param name="spmr" 165 <param name="spmr"
160 type="boolean" truevalue="--SPMR" falsevalue="" checked="False" 166 type="boolean" truevalue="--SPMR" falsevalue="" checked="False"
161 label="Save signal per million reads for fragment pileup profiles" 167 label="Save signal per million reads for fragment pileup profiles"
162 help="(--SPMR)" /> 168 help="(--SPMR)" />
169 <param name="make_bigwig" type="boolean" checked="True"
170 truevalue="True" falsevalue=""
171 label="Also generate bigWig file from bedGraph"
172 help="bigWig file can used in subsequent analyses e.g. CEAS" />
163 </when> 173 </when>
164 <when value=""> 174 <when value="">
165 <!-- Display nothing --> 175 <!-- Display nothing -->
166 </when> 176 </when>
167 </conditional> 177 </conditional>
298 <data name="output_lambda_bedgraph_file" format="bedgraph" 308 <data name="output_lambda_bedgraph_file" format="bedgraph"
299 label="${tool.name}: callpeak on ${on_string} (control lambda: bedGraph)"> 309 label="${tool.name}: callpeak on ${on_string} (control lambda: bedGraph)">
300 <filter>major_command['bdg_options']['bdg'] is True</filter> 310 <filter>major_command['bdg_options']['bdg'] is True</filter>
301 <filter>major_command['major_command_selector'] == 'callpeak'</filter> 311 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
302 </data> 312 </data>
313 <data name="output_bigwig_file" format="bigwig"
314 label="${tool.name}: callpeak on ${on_string} (treat pileup: bigWig)">
315 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
316 <filter>major_command['bdg_options']['bdg'] is True</filter>
317 <filter>major_command['bdg_options']['make_bigwig'] is True</filter>
318 </data>
303 <!--bdgcmp output--> 319 <!--bdgcmp output-->
304 <data name="output_bdgcmp_file" format="bdg" 320 <data name="output_bdgcmp_file" format="bdg"
305 label="${tool.name}: bdgcmp on ${on_string} (bdg)"> 321 label="${tool.name}: bdgcmp on ${on_string} (bdg)">
306 <filter>major_command['major_command_selector'] == 'bdgcmp'</filter> 322 <filter>major_command['major_command_selector'] == 'bdgcmp'</filter>
307 </data> 323 </data>