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comparison diffbind.xml @ 14:c97a786e8fb5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
author iuc
date Thu, 07 Jun 2018 05:21:22 -0400
parents 1de83981d43c
children 194e3f2c1d86
comparison
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13:1de83981d43c 14:c97a786e8fb5
1 <tool id="diffbind" name="DiffBind" version="2.6.6.3"> 1 <tool id="diffbind" name="DiffBind" version="2.6.6.4">
2 <description> differential binding analysis of ChIP-Seq peak data</description> 2 <description> differential binding analysis of ChIP-Seq peak data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.6.6">bioconductor-diffbind</requirement> 4 <requirement type="package" version="2.6.6">bioconductor-diffbind</requirement>
5 <requirement type="package" version="1.20.0">r-getopt</requirement> 5 <requirement type="package" version="1.20.0">r-getopt</requirement>
6 <requirement type="package" version="0.2.15">r-rjson</requirement> 6 <requirement type="package" version="0.2.15">r-rjson</requirement>
35 #set $peak_files = list() 35 #set $peak_files = list()
36 #set $bam_files = list() 36 #set $bam_files = list()
37 #set $bam_controls = list() 37 #set $bam_controls = list()
38 38
39 #for $file in $g.peaks: 39 #for $file in $g.peaks:
40 #set $file_name = re.sub('[^\w\-\s]', '_', str($file.element_identifier)) 40 #set $file_name = str($g.groupName) + "-" + re.sub('[^\w\-]', '_', str($file.element_identifier)) + "-peaks.bed"
41 ln -s '${file}' ${g.groupName}-${file_name}-peaks.bed && 41 ln -s '${file}' '${file_name}' &&
42 $peak_files.append(str($g.groupName) + '-' + $file_name + '-peaks.bed') 42 $peak_files.append($file_name)
43 #end for 43 #end for
44 44
45 #for $bam in $g.bamreads: 45 #for $bam in $g.bamreads:
46 #set $bam_name = re.sub('[^\w\-\s]', '_', str($bam.element_identifier)) 46 #set $bam_name = re.sub('[^\w\-]', '_', str($bam.element_identifier))
47 ln -s '${bam}' ${bam_name}-bamreads.bam && 47 #set $bam_file = $bam_name + "-bamreads.bam"
48 ln -s ${bam.metadata.bam_index} ${bam_name}-bamreads.bai && 48 #set $bam_index = $bam_name + "-bamreads.bai"
49 $bam_files.append($bam_name + '-bamreads.bam') 49 ln -s '${bam}' '${bam_file}' &&
50 ln -s '${bam.metadata.bam_index}' '${bam_index}' &&
51 $bam_files.append($bam_file)
50 #end for 52 #end for
51 53
52 $temp_factor.append( {str($g.groupName): $peak_files} ) 54 $temp_factor.append( {str($g.groupName): $peak_files} )
53 $temp_factor.append( {str($g.groupName): $bam_files} ) 55 $temp_factor.append( {str($g.groupName): $bam_files} )
54 56
55 #if str( $g.bamcontrol ) != 'None': 57 #if str( $g.bamcontrol ) != 'None':
56 #for $ctrl in $g.bamcontrol: 58 #for $ctrl in $g.bamcontrol:
57 #set $ctrl_name = re.sub('[^\w\-\s]', '_', str($ctrl.element_identifier)) 59 #set $ctrl_name = re.sub('[^\w\-]', '_', str($ctrl.element_identifier))
58 ln -s '${ctrl}' ${g.groupName}-${ctrl_name}-bamcontrol.bam && 60 #set $ctrl_file = $ctrl_name + "-bamcontrol.bam"
59 ln -s ${ctrl.metadata.bam_index} ${g.groupName}-${ctrl_name}-bamcontrol.bai && 61 #set ctrl_index = $ctrl_name + "-bamcontrol.bai"
60 $bam_controls.append(str($g.groupName) + '-' + $ctrl_name + '-bamcontrol.bam') 62 #if $ctrl_file not in json.dumps($temp_factor):
63 ln -s '${ctrl}' '${ctrl_file}' &&
64 ln -s '${ctrl.metadata.bam_index}' '${ctrl_index}' &&
65 #end if
66 $bam_controls.append($ctrl_file)
61 #end for 67 #end for
62 $temp_factor.append( {str($g.groupName): $bam_controls} ) 68 $temp_factor.append( {str($g.groupName): $bam_controls} )
63 #end if 69 #end if
64 70
65 #end for 71 #end for
111 <valid initial="string.letters,string.digits"><add value="_" /></valid> 117 <valid initial="string.letters,string.digits"><add value="_" /></valid>
112 </sanitizer> 118 </sanitizer>
113 <validator type="empty_field" /> 119 <validator type="empty_field" />
114 </param> 120 </param>
115 <param name="peaks" type="data" format="bed" multiple="true" label="Peak files" help="Result of your Peak calling experiment"/> 121 <param name="peaks" type="data" format="bed" multiple="true" label="Peak files" help="Result of your Peak calling experiment"/>
116 <param name="bamreads" type="data" format="bam" multiple="true" label="Read BAM file" help="Specify the Read BAM file used in the Peak calling."/> 122 <param name="bamreads" type="data" format="bam" multiple="true" label="Read BAM files" help="Specify the Read BAM files used in the Peak calling. The input order of the BAM files for the samples MUST match the input order of the peaks files."/>
117 <param name="bamcontrol" type="data" format="bam" multiple="true" optional="True" label="Control BAM file" help="If specifying a control BAM file, all samples are required to specify one, see Help section below."/> 123 <param name="bamcontrol" type="data" format="bam" multiple="true" optional="True" label="Control BAM files" help="If specifying a control BAM file, all samples are required to specify one, see Help section below. The input order of the BAM files for the samples MUST match the input order of the peaks files."/>
118 </repeat> 124 </repeat>
119 125
120 <param name="scorecol" type="integer" min="0" value="8" label="Score Column" help="Column in peak files that contains peak scores. Default: 8 (narrowPeak)"> 126 <param name="scorecol" type="integer" min="0" value="8" label="Score Column" help="Column in peak files that contains peak scores. Default: 8 (narrowPeak)">
121 <sanitizer> 127 <sanitizer>
122 <valid initial="string.digits"/> 128 <valid initial="string.digits"/>
202 <assert_contents> 208 <assert_contents>
203 <has_text text="SessionInfo"/> 209 <has_text text="SessionInfo"/>
204 </assert_contents> 210 </assert_contents>
205 </output> 211 </output>
206 </test> 212 </test>
213 <!-- Ensure control BAMs input works -->
214 <test expect_num_outputs="1">
215 <repeat name="rep_group">
216 <param name="groupName" value="Resistant"/>
217 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
218 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
219 <param name="bamcontrol" ftype="bam" value="input1.bam,input2.bam" />
220 </repeat>
221 <repeat name="rep_group">
222 <param name="groupName" value="Responsive"/>
223 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
224 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
225 <param name="bamcontrol" ftype="bam" value="input1.bam,input2.bam" />
226 </repeat>
227 <param name="scorecol" value="5" />
228 <param name="format" value="interval"/>
229 <output name="outfile" ftype="interval" value="out_diffbind_ctrl.interval" />
230 </test>
207 <!-- Ensure BED output works --> 231 <!-- Ensure BED output works -->
208 <test expect_num_outputs="1"> 232 <test expect_num_outputs="1">
209 <repeat name="rep_group"> 233 <repeat name="rep_group">
210 <param name="groupName" value="Resistant"/> 234 <param name="groupName" value="Resistant"/>
211 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> 235 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
264 affinity data, the second working through the main plotting routines, the third discussing the 288 affinity data, the second working through the main plotting routines, the third discussing the
265 use of a blocking factor, and the fourth revisiting occupancy data (peak calls) in more detail, 289 use of a blocking factor, and the fourth revisiting occupancy data (peak calls) in more detail,
266 as well as comparing the results of an occupancy-based analysis with an affinity-based one. 290 as well as comparing the results of an occupancy-based analysis with an affinity-based one.
267 Finally, certain technical aspects of the how these analyses are accomplished are detailed. 291 Finally, certain technical aspects of the how these analyses are accomplished are detailed.
268 292
269 Note this DiffBind tool requires a minimum of four samples (two groups with two replicates each). 293 **Note this DiffBind tool requires a minimum of four samples (two groups with two replicates each).**
270 294
271 ----- 295 -----
272 296
273 **Inputs** 297 **Inputs**
274 298