Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.xml @ 94:84e9e5c8c101 draft

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"planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
author rhpvorderman
date Fri, 24 Mar 2023 16:58:28 +0000
parents 8fcf31272f6e
children d63eff357515
comparison
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93:8fcf31272f6e 94:84e9e5c8c101
1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.7.0" profile="16.04"> 1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.8.0" 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.
26 ln -s "$in_file" "$input" && 26 ln -s "$in_file" "$input" &&
27 #if str ( $filter_unique.filter_unique_select ) == "remove": 27 #if str ( $filter_unique.filter_unique_select ) == "remove":
28 $__tool_directory__/wrapper.sh "$input" 28 $__tool_directory__/wrapper.sh "$input"
29 custom $out_file $out_file.files_path 29 custom $out_file $out_file.files_path
30 "${in_file.name}" "-" $functionality $unique 30 "${in_file.name}" "-" $functionality $unique
31 $naive_output_cond.naive_output $naive_output_ca 31 $naive_output_cond.naive_output $naive_output_ca $naive_output_cg
32 $naive_output_cg $naive_output_cm $naive_output_ce 32 $naive_output_cm $naive_output_ce $naive_output_all $naive_output_igm_naive
33 $naive_output_all $filter_unique.filter_unique_select 33 $naive_output_igm_naive_memory
34 $filter_unique.filter_unique_select
34 $filter_unique.filter_unique_clone_count 35 $filter_unique.filter_unique_clone_count
35 $class_filter_cond.class_filter 36 $class_filter_cond.class_filter
36 $empty_region_filter 37 $empty_region_filter
37 $fast 38 $fast
38 #else: 39 #else:
39 $__tool_directory__/wrapper.sh 40 $__tool_directory__/wrapper.sh
40 "$input" custom 41 "$input" custom
41 $out_file $out_file.files_path 42 $out_file $out_file.files_path
42 "${in_file.name}" "-" $functionality $unique 43 "${in_file.name}" "-" $functionality $unique
43 $naive_output_cond.naive_output $naive_output_ca $naive_output_cg 44 $naive_output_cond.naive_output $naive_output_ca $naive_output_cg
44 $naive_output_cm $naive_output_ce $naive_output_all 45 $naive_output_cm $naive_output_ce $naive_output_all $naive_output_igm_naive
46 $naive_output_igm_naive_memory
45 $filter_unique.filter_unique_select 47 $filter_unique.filter_unique_select
46 2 48 2
47 $class_filter_cond.class_filter 49 $class_filter_cond.class_filter
48 $empty_region_filter 50 $empty_region_filter
49 $fast 51 $fast
98 <option value="70_0">>70% class</option> 100 <option value="70_0">>70% class</option>
99 <option value="60_0">>60% class</option> 101 <option value="60_0">>60% class</option>
100 <option value="19_0">>19% class</option> 102 <option value="19_0">>19% class</option>
101 <option value="101_101_all">Do not assign (sub)class</option> 103 <option value="101_101_all">Do not assign (sub)class</option>
102 <option value="101_101_IGM">Everything is IGM</option> 104 <option value="101_101_IGM">Everything is IGM</option>
105 <option value="101_101_IGA">Everything is IGA</option>
106 <option value="101_101_IGG">Everything is IGG</option>
103 </param> 107 </param>
104 </conditional> 108 </conditional>
105 <conditional name="naive_output_cond"> 109 <conditional name="naive_output_cond">
106 <param name="naive_output" type="select" label="Output new IMGT archives per class into your history?"> 110 <param name="naive_output" type="select" label="Output new IMGT archives per class into your history?">
107 <option value="yes">Yes</option> 111 <option value="yes">Yes</option>
118 <outputs> 122 <outputs>
119 <data format="html" name="out_file" label = "SHM &amp; CSR on ${in_file.name}"/> 123 <data format="html" name="out_file" label = "SHM &amp; CSR on ${in_file.name}"/>
120 <data format="imgt_archive" name="naive_output_ca" label = "Filtered IMGT IGA: ${in_file.name}" > 124 <data format="imgt_archive" name="naive_output_ca" label = "Filtered IMGT IGA: ${in_file.name}" >
121 <filter>naive_output_cond['naive_output'] == "yes"</filter> 125 <filter>naive_output_cond['naive_output'] == "yes"</filter>
122 <filter>class_filter_cond['class_filter'] != "101_101"</filter> 126 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
127 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
128 <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter>
123 </data> 129 </data>
124 <data format="imgt_archive" name="naive_output_cg" label = "Filtered IMGT IGG: ${in_file.name}" > 130 <data format="imgt_archive" name="naive_output_cg" label = "Filtered IMGT IGG: ${in_file.name}" >
125 <filter>naive_output_cond['naive_output'] == "yes"</filter> 131 <filter>naive_output_cond['naive_output'] == "yes"</filter>
126 <filter>class_filter_cond['class_filter'] != "101_101"</filter> 132 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
133 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
134 <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter>
127 </data> 135 </data>
128 <data format="imgt_archive" name="naive_output_cm" label = "Filtered IMGT IGM: ${in_file.name}" > 136 <data format="imgt_archive" name="naive_output_cm" label = "Filtered IMGT IGM: ${in_file.name}" >
129 <filter>naive_output_cond['naive_output'] == "yes"</filter> 137 <filter>naive_output_cond['naive_output'] == "yes"</filter>
130 <filter>class_filter_cond['class_filter'] != "101_101"</filter> 138 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
139 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
140 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
131 </data> 141 </data>
132 <data format="imgt_archive" name="naive_output_ce" label = "Filtered IMGT IGE: ${in_file.name}" > 142 <data format="imgt_archive" name="naive_output_ce" label = "Filtered IMGT IGE: ${in_file.name}" >
133 <filter>naive_output_cond['naive_output'] == "yes"</filter> 143 <filter>naive_output_cond['naive_output'] == "yes"</filter>
134 <filter>class_filter_cond['class_filter'] != "101_101"</filter> 144 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
145 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
146 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
147 <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter>
148 </data>
149 <data format="imgt archive" name="naive_output_igm_naive" label = "Filtered naive IGM sequences (mutations below 2%): ${in_file.name}">
150 <filter>naive_output_cond['naive_output'] == "yes"</filter>
151 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
152 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
153 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
154 </data>
155 <data format="imgt archive" name="naive_output_igm_naive_memory" label = "Filtered naive memory IGM sequences (mutations over 2%): ${in_file.name}">
156 <filter>naive_output_cond['naive_output'] == "yes"</filter>
157 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
158 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
159 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
135 </data> 160 </data>
136 <data format="imgt_archive" name="naive_output_all" label = "Filtered IMGT all: ${in_file.name}" > 161 <data format="imgt_archive" name="naive_output_all" label = "Filtered IMGT all: ${in_file.name}" >
137 <filter>naive_output_cond['naive_output'] == "yes"</filter> 162 <filter>naive_output_cond['naive_output'] == "yes"</filter>
138 <filter>class_filter_cond['class_filter'] == "101_101"</filter> 163 <filter>class_filter_cond['class_filter'] == "101_101"</filter>
139 </data> 164 </data>