Mercurial > repos > bgruening > deeptools_bam_compare

comparison bamCompare.xml @ 8:89f6d2283317 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
author bgruening
date Tue, 20 Sep 2016 03:06:21 -0400
parents 8e41fe2f3661
children 8f2a1286b61c
comparison
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7:d5d57b40b29a 8:89f6d2283317
63 $advancedOpt.skipNAs 63 $advancedOpt.skipNAs
64 64
65 #if str($advancedOpt.ignoreForNormalization).strip() != '': 65 #if str($advancedOpt.ignoreForNormalization).strip() != '':
66 --ignoreForNormalization '$advancedOpt.ignoreForNormalization' 66 --ignoreForNormalization '$advancedOpt.ignoreForNormalization'
67 #end if 67 #end if
68
69 @blacklist@
68 #end if 70 #end if
69 ]]> 71 ]]>
70 </command> 72 </command>
71 <inputs> 73 <inputs>
72 <param argument="--bamFile1" format="bam" type="data" label="First BAM file (e.g. treated sample)" 74 <param argument="--bamFile1" format="bam" type="data" label="First BAM file (e.g. treated sample)"
103 <conditional name="comparison"> 105 <conditional name="comparison">
104 <param name="type" type="select" 106 <param name="type" type="select"
105 label="How to compare the two files" 107 label="How to compare the two files"
106 help="The default is to output the log2ratio between the two samples. 108 help="The default is to output the log2ratio between the two samples.
107 The reciprocal ratio returns the negative of the inverse of the ratio if 109 The reciprocal ratio returns the negative of the inverse of the ratio if
108 the ratio is less than 0. The resulting values are interpreted as negative fold changes."> 110 the ratio is less than 0. The resulting values are interpreted as negative
111 fold changes. To output the scaled values from the first or second BAM file,
112 select 'first' or 'second'.">
109 <option value="log2" selected="true">Compute log2 of the number of reads ratio</option> 113 <option value="log2" selected="true">Compute log2 of the number of reads ratio</option>
110 <option value="ratio">Compute the ratio of the number of reads</option> 114 <option value="ratio">Compute the ratio of the number of reads</option>
111 <option value="subtract">Compute difference (subtract input from treatment) of the number of reads</option> 115 <option value="subtract">Compute difference (subtract input from treatment) of the number of reads</option>
112 <option value="add">Compute the sum of number of reads</option> 116 <option value="add">Compute the sum of number of reads</option>
113 <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option> 117 <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option>
118 <option value="first">Returns the scaled value of the first BAM file</option>
119 <option value="second">Returns the scaled value of the second BAM file</option>
114 </param> 120 </param>
115 <when value="log2"> 121 <when value="log2">
116 <expand macro="pseudocount" /> 122 <expand macro="pseudocount" />
117 </when> 123 </when>
118 <when value="ratio"> 124 <when value="ratio">
119 <expand macro="pseudocount" /> 125 <expand macro="pseudocount" />
120 </when> 126 </when>
121 <when value="add" /> 127 <when value="add" />
128 <when value="first" />
129 <when value="second" />
122 <when value="reciprocal_ratio"> 130 <when value="reciprocal_ratio">
123 <expand macro="pseudocount" /> 131 <expand macro="pseudocount" />
124 </when> 132 </when>
125 <when value="subtract"> 133 <when value="subtract">
126 <conditional name="normalization"> 134 <conditional name="normalization">
152 <when value="yes"> 160 <when value="yes">
153 <expand macro="smoothLength" /> 161 <expand macro="smoothLength" />
154 <expand macro="read_processing_options" /> 162 <expand macro="read_processing_options" />
155 163
156 <expand macro="skipNAs" /> 164 <expand macro="skipNAs" />
165
157 <param argument="--ignoreForNormalization" type="text" value="" size="50" 166 <param argument="--ignoreForNormalization" type="text" value="" size="50"
158 label="regions that should be excluded for calculating the scaling factor" 167 label="regions that should be excluded for calculating the scaling factor"
159 help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. 168 help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor.
160 For example, if you know of copy number variations between samples then you may want to exclude these. 169 For example, if you know of copy number variations between samples then you may want to exclude these.
161 Another typical example is the difference in chromosome X copies between males and females in many species. 170 Another typical example is the difference in chromosome X copies between males and females in many species.
162 Example inputs are chrX,chrY,chr3 or chr10:12220-128932" /> 171 Example inputs are chrX,chrY,chr3 or chr10:12220-128932" />
172 <expand macro="blacklist" />
163 </when> 173 </when>
164 </conditional> 174 </conditional>
165 </inputs> 175 </inputs>
166 <outputs> 176 <outputs>
167 <data format="bigwig" name="outFileName"> 177 <data format="bigwig" name="outFileName">