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comparison shm_csr.xml @ 98:d714f5ea83d7 draft default tip

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planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
author rhpvorderman
date Wed, 10 Jan 2024 12:32:47 +0000
parents fbc6307dd83b
children
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97:fbc6307dd83b 98:d714f5ea83d7
1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.9.1" profile="16.04"> 1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.10.0" profile="16.04">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.7.1">python</requirement> 4 <requirement type="package" version="3.7.1">python</requirement>
5 <requirement type="package" version="0.4.4">changeo</requirement> 5 <requirement type="package" version="0.4.4">changeo</requirement>
6 <!--Biopython should be set at a version at the release of changeo 0.4.4. 6 <!--Biopython should be set at a version at the release of changeo 0.4.4.
33 $naive_output_igm_naive_memory 33 $naive_output_igm_naive_memory
34 $filter_unique.filter_unique_select 34 $filter_unique.filter_unique_select
35 $filter_unique.filter_unique_clone_count 35 $filter_unique.filter_unique_clone_count
36 $class_filter_cond.class_filter 36 $class_filter_cond.class_filter
37 $empty_region_filter 37 $empty_region_filter
38 $fast 38 $changeo $baseline
39 #else: 39 #else:
40 $__tool_directory__/wrapper.sh "$in_file" 40 $__tool_directory__/wrapper.sh "$in_file"
41 custom 41 custom
42 $out_file $out_file.files_path 42 $out_file $out_file.files_path
43 "${in_file.name}" "-" $functionality $unique 43 "${in_file.name}" "-" $functionality $unique
46 $naive_output_igm_naive_memory 46 $naive_output_igm_naive_memory
47 $filter_unique.filter_unique_select 47 $filter_unique.filter_unique_select
48 2 48 2
49 $class_filter_cond.class_filter 49 $class_filter_cond.class_filter
50 $empty_region_filter 50 $empty_region_filter
51 $fast 51 $changeo $baseline
52 #end if 52 #end if
53 ]]> 53 ]]>
54 </command> 54 </command>
55 <inputs> 55 <inputs>
56 <param name="in_file" type="data" format="data" label="IMGT zip file to be analysed" /> 56 <param name="in_file" type="data" format="data" label="IMGT zip file to be analysed" />
106 <option value="101_101_IGA">Everything is IGA</option> 106 <option value="101_101_IGA">Everything is IGA</option>
107 <option value="101_101_IGG">Everything is IGG</option> 107 <option value="101_101_IGG">Everything is IGG</option>
108 </param> 108 </param>
109 </conditional> 109 </conditional>
110 <conditional name="naive_output_cond"> 110 <conditional name="naive_output_cond">
111 <param name="naive_output" type="select" label="Output new IMGT archives per class into your history?"> 111 <param name="naive_output" type="boolean" label="Output new IMGT archives per class into your history?"
112 <option value="yes">Yes</option> 112 checked="no" truevalue="yes" falsevalue="no"/>
113 <option value="no" selected="true">No</option> 113 </conditional>
114 </param> 114 <param name="changeo" type="boolean" label="Run Change-O"
115 <when value="yes"></when> 115 checked="yes" truevalue="yes" falsevalue="no"/>
116 <when value="no"></when> 116 <param name="baseline" type="boolean" label="Run Baseline"
117 </conditional> 117 checked="yes" truevalue="yes" falsevalue="no"
118 <param name="fast" type="select" label="Fast" help="Skips Change-O/Baseline" > 118 help="Baseline is automatically skipped when functionality filter is set to unproductive only."
119 <option value="yes">Yes</option> 119 />
120 <option value="no" selected="true">No</option>
121 </param>
122 </inputs> 120 </inputs>
123 <outputs> 121 <outputs>
124 <data format="html" name="out_file" label = "SHM &amp; CSR on ${in_file.name}"/> 122 <data format="html" name="out_file" label = "SHM &amp; CSR on ${in_file.name}"/>
125 <data format="imgt_archive" name="naive_output_ca" label = "Filtered IMGT IGA: ${in_file.name}" > 123 <data format="imgt_archive" name="naive_output_ca" label = "Filtered IMGT IGA: ${in_file.name}" >
126 <filter>naive_output_cond['naive_output'] == "yes"</filter> 124 <filter>naive_output_cond['naive_output'] is True</filter>
127 <filter>class_filter_cond['class_filter'] != "101_101"</filter> 125 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
128 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter> 126 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
129 <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter> 127 <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter>
130 </data> 128 </data>
131 <data format="imgt_archive" name="naive_output_cg" label = "Filtered IMGT IGG: ${in_file.name}" > 129 <data format="imgt_archive" name="naive_output_cg" label = "Filtered IMGT IGG: ${in_file.name}" >
132 <filter>naive_output_cond['naive_output'] == "yes"</filter> 130 <filter>naive_output_cond['naive_output'] is True</filter>
133 <filter>class_filter_cond['class_filter'] != "101_101"</filter> 131 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
134 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter> 132 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
135 <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter> 133 <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter>
136 </data> 134 </data>
137 <data format="imgt_archive" name="naive_output_cm" label = "Filtered IMGT IGM: ${in_file.name}" > 135 <data format="imgt_archive" name="naive_output_cm" label = "Filtered IMGT IGM: ${in_file.name}" >
138 <filter>naive_output_cond['naive_output'] == "yes"</filter> 136 <filter>naive_output_cond['naive_output'] is True</filter>
139 <filter>class_filter_cond['class_filter'] != "101_101"</filter> 137 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
140 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter> 138 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
141 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter> 139 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
142 </data> 140 </data>
143 <data format="imgt_archive" name="naive_output_ce" label = "Filtered IMGT IGE: ${in_file.name}" > 141 <data format="imgt_archive" name="naive_output_ce" label = "Filtered IMGT IGE: ${in_file.name}" >
144 <filter>naive_output_cond['naive_output'] == "yes"</filter> 142 <filter>naive_output_cond['naive_output'] is True</filter>
145 <filter>class_filter_cond['class_filter'] != "101_101"</filter> 143 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
146 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter> 144 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
147 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter> 145 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
148 <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter> 146 <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter>
149 </data> 147 </data>
150 <data format="imgt_archive" name="naive_output_igm_naive" label = "Filtered naive IGM sequences (mutations below 2%): ${in_file.name}"> 148 <data format="imgt_archive" name="naive_output_igm_naive" label = "Filtered naive IGM sequences (mutations below 2%): ${in_file.name}">
151 <filter>naive_output_cond['naive_output'] == "yes"</filter> 149 <filter>naive_output_cond['naive_output'] is True</filter>
152 <filter>class_filter_cond['class_filter'] != "101_101"</filter> 150 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
153 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter> 151 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
154 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter> 152 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
155 </data> 153 </data>
156 <data format="imgt_archive" name="naive_output_igm_naive_memory" label = "Filtered naive memory IGM sequences (mutations over 2%): ${in_file.name}"> 154 <data format="imgt_archive" name="naive_output_igm_naive_memory" label = "Filtered naive memory IGM sequences (mutations over 2%): ${in_file.name}">
157 <filter>naive_output_cond['naive_output'] == "yes"</filter> 155 <filter>naive_output_cond['naive_output'] is True</filter>
158 <filter>class_filter_cond['class_filter'] != "101_101"</filter> 156 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
159 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter> 157 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
160 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter> 158 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
161 </data> 159 </data>
162 <data format="imgt_archive" name="naive_output_all" label = "Filtered IMGT all: ${in_file.name}" > 160 <data format="imgt_archive" name="naive_output_all" label = "Filtered IMGT all: ${in_file.name}" >
163 <filter>naive_output_cond['naive_output'] == "yes"</filter> 161 <filter>naive_output_cond['naive_output'] is True</filter>
164 <filter>class_filter_cond['class_filter'] == "101_101"</filter> 162 <filter>class_filter_cond['class_filter'] == "101_101"</filter>
165 </data> 163 </data>
166 </outputs> 164 </outputs>
167 <tests> 165 <tests>
168 <test> 166 <test>