Mercurial > repos > davidvanzessen > shm_csr
diff shm_csr.xml @ 94:84e9e5c8c101 draft
"planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
| author | rhpvorderman |
|---|---|
| date | Fri, 24 Mar 2023 16:58:28 +0000 |
| parents | 8fcf31272f6e |
| children | d63eff357515 |
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--- a/shm_csr.xml Mon Mar 06 11:36:32 2023 +0000 +++ b/shm_csr.xml Fri Mar 24 16:58:28 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="shm_csr" name="SHM & CSR pipeline" version="1.7.0" profile="16.04"> +<tool id="shm_csr" name="SHM & CSR pipeline" version="1.8.0" profile="16.04"> <description></description> <requirements> <requirement type="package" version="3.7.1">python</requirement> @@ -28,9 +28,10 @@ $__tool_directory__/wrapper.sh "$input" custom $out_file $out_file.files_path "${in_file.name}" "-" $functionality $unique - $naive_output_cond.naive_output $naive_output_ca - $naive_output_cg $naive_output_cm $naive_output_ce - $naive_output_all $filter_unique.filter_unique_select + $naive_output_cond.naive_output $naive_output_ca $naive_output_cg + $naive_output_cm $naive_output_ce $naive_output_all $naive_output_igm_naive + $naive_output_igm_naive_memory + $filter_unique.filter_unique_select $filter_unique.filter_unique_clone_count $class_filter_cond.class_filter $empty_region_filter @@ -41,7 +42,8 @@ $out_file $out_file.files_path "${in_file.name}" "-" $functionality $unique $naive_output_cond.naive_output $naive_output_ca $naive_output_cg - $naive_output_cm $naive_output_ce $naive_output_all + $naive_output_cm $naive_output_ce $naive_output_all $naive_output_igm_naive + $naive_output_igm_naive_memory $filter_unique.filter_unique_select 2 $class_filter_cond.class_filter @@ -100,6 +102,8 @@ <option value="19_0">>19% class</option> <option value="101_101_all">Do not assign (sub)class</option> <option value="101_101_IGM">Everything is IGM</option> + <option value="101_101_IGA">Everything is IGA</option> + <option value="101_101_IGG">Everything is IGG</option> </param> </conditional> <conditional name="naive_output_cond"> @@ -120,18 +124,39 @@ <data format="imgt_archive" name="naive_output_ca" label = "Filtered IMGT IGA: ${in_file.name}" > <filter>naive_output_cond['naive_output'] == "yes"</filter> <filter>class_filter_cond['class_filter'] != "101_101"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter> </data> <data format="imgt_archive" name="naive_output_cg" label = "Filtered IMGT IGG: ${in_file.name}" > <filter>naive_output_cond['naive_output'] == "yes"</filter> <filter>class_filter_cond['class_filter'] != "101_101"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter> </data> <data format="imgt_archive" name="naive_output_cm" label = "Filtered IMGT IGM: ${in_file.name}" > <filter>naive_output_cond['naive_output'] == "yes"</filter> <filter>class_filter_cond['class_filter'] != "101_101"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter> </data> <data format="imgt_archive" name="naive_output_ce" label = "Filtered IMGT IGE: ${in_file.name}" > <filter>naive_output_cond['naive_output'] == "yes"</filter> <filter>class_filter_cond['class_filter'] != "101_101"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter> + </data> + <data format="imgt archive" name="naive_output_igm_naive" label = "Filtered naive IGM sequences (mutations below 2%): ${in_file.name}"> + <filter>naive_output_cond['naive_output'] == "yes"</filter> + <filter>class_filter_cond['class_filter'] != "101_101"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter> + </data> + <data format="imgt archive" name="naive_output_igm_naive_memory" label = "Filtered naive memory IGM sequences (mutations over 2%): ${in_file.name}"> + <filter>naive_output_cond['naive_output'] == "yes"</filter> + <filter>class_filter_cond['class_filter'] != "101_101"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter> </data> <data format="imgt_archive" name="naive_output_all" label = "Filtered IMGT all: ${in_file.name}" > <filter>naive_output_cond['naive_output'] == "yes"</filter>