Mercurial > repos > vijay > pancancer_apply_weights

annotate macros.xml @ 0:3543d3e66ecb draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
author vijay
date Wed, 16 Dec 2020 23:30:39 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
1 <macros>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
2 <token name="@VERSION@">0.1.9</token>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
3
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
4 <xml name="requirements">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
5 <requirements>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
6 <requirement type="package" version="@VERSION@">papaa</requirement>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
7 </requirements>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
8 </xml>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
9
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
10 <xml name="stdio">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
11 <stdio>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
12 <exit_code level="fatal" range="1:"/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
13 </stdio>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
14 </xml>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
15
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
16 <xml name="inputs_basic">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
17 <param argument="--x_matrix" label="Filename of features to use in model" name="x_matrix" optional="true" type="data" format="tabular" help="data/pancan_rnaseq_freeze.tsv.gz"/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
18 <yield/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
19 <param argument="--filename_mut" label="Filename mutations" name="filename_mut" optional="true" type="data" format="tabular" help="data/pancan_mutation_freeze.tsv.gz"/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
20 <param argument="--filename_mut_burden" label="Filename of mutation burden" name="filename_mut_burden" optional="true" type="data" format="tabular" help="data/mutation_burden_freeze.tsv"/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
21 <param argument="--filename_sample" label="Filename of sample" name="filename_sample" optional="true" type="data" format="tabular" help="data/sample_freeze.tsv"/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
22 </xml>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
23
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
24 <token name="@INPUTS_BASIC@"><![CDATA[
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
25 #if $x_matrix and $x_matrix is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
26 --x_matrix '$x_matrix'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
27 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
28 #if $filename_mut and $filename_mut is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
29 --filename_mut '$filename_mut'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
30 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
31 #if $filename_mut_burden and $filename_mut_burden is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
32 --filename_mut_burden '$filename_mut_burden'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
33 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
34 #if $filename_sample and $filename_sample is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
35 --filename_sample '$filename_sample'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
36 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
37 ]]>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
38 </token>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
39
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
40 <xml name="inputs_genes_diseases">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
41 <param argument="--genes" label="Comma separated string of HUGO gene symbols" name="genes" optional="False" type="text" value="ERBB2,PIK3CA,KRAS,AKT1"/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
42 <param argument="--diseases" label="Comma sep string of TCGA disease acronyms. If no arguments are passed, filtering will default to options given in --filter_count and --filter_prop." name="diseases" optional="true" type="text" value="BLCA,BRCA,CESC,COAD,ESCA,LUAD,LUSC,OV,PRAD,READ,STAD,UCEC,UCS"/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
43 </xml>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
44
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
45 <token name="@INPUTS_GENES_DISEASES@"><![CDATA[
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
46 #if $genes and $genes is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
47 --genes '$genes'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
48 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
49 #if $diseases and str($diseases) != '':
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
50 --diseases '$diseases'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
51 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
52 ]]>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
53 </token>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
54
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
55
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
56 <xml name="input_filename_raw_mut">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
57 <param argument="--filename_raw_mut" label="Filename of raw mut MAF" name="filename_raw_mut" optional="true" type="data" format="tabular" help="data/raw/mc3.v0.2.8.PUBLIC.maf"/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
58 </xml>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
59
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
60 <token name="@INPUT_FILENAME_RAW_MUT@"><![CDATA[
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
61 #if $filename_raw_mut and $filename_raw_mut is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
62 --filename_raw_mut '$filename_raw_mut'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
63 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
64 ]]>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
65 </token>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
66
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
67
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
68 <xml name="input_filename_burden">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
69 <param argument="--filename_burden" label="Burden file" name="filename_burden" optional="true" type="data" format="tabular" help="data/seg_based_scores.tsv"/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
70 </xml>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
71
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
72 <token name="@INPUT_FILENAME_BURDEN@"><![CDATA[
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
73 #if $filename_burden and $filename_burden is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
74 --filename_burden '$filename_burden'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
75 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
76 ]]>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
77 </token>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
78
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
79 <xml name="input_filename_snaptron_samples">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
80 <param argument="--sample_file" label="SNAPTRON samples" name="sample_file" optional="true" type="data" format="tabular" help="scripts/snaptron/samples.tsv.gz"/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
81 </xml>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
82
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
83 <token name="@INPUT_FILENAME_SNAPTRON_SAMPLES@"><![CDATA[
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
84 #if $sample_file and $sample_file is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
85 --sample_file '$sample_file'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
86 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
87 ]]>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
88 </token>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
89
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
90
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
91 <xml name="input_filename_snaptron_junctions">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
92 <param argument="--junction_file" label="SNAPTRON junctions" name="junction_file" optional="true" type="data" format="tabular" help="scripts/snaptron/tp53_junctions.txt.gz"/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
93 </xml>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
94
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
95 <token name="@INPUT_FILENAME_SNAPTRON_JUNCTIONS@"><![CDATA[
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
96 #if $junction_file and $junction_file is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
97 --junction_file '$junction_file'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
98 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
99 ]]>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
100 </token>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
101
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
102 <xml name="inputs_copy_number_file">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
103 <param argument="--filename_copy_loss" label="File with Copy number loss" name="filename_copy_loss" optional="true" type="data" format="tabular" help="data/copy_number_loss_status.tsv.gz"/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
104 <param argument="--filename_copy_gain" label="File with Copy number gain" name="filename_copy_gain" optional="true" type="data" format="tabular" help="data/copy_number_gain_status.tsv.gz"/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
105 </xml>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
106
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
107 <xml name="inputs_copy_number_class_file">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
108 <expand macro="inputs_copy_number_file" />
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
109 <param argument="--filename_cancer_gene_classification" label="File with cancer gene classification table" name="filename_cancer_gene_classification" optional="true" type="data" format="tabular" help="data/cosmic_cancer_classification.tsv"/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
110 </xml>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
111
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
112 <xml name="inputs_copy_number_file_conditional">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
113 <conditional name="copy_number_conditional">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
114 <param argument="--copy_number" checked="false" label="Supplement Y matrix with copy number events" name="copy_number" type="boolean" truevalue="--copy_number" falsevalue=""/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
115 <when value="--copy_number">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
116 <expand macro="inputs_copy_number_file" />
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
117 </when>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
118 <when value=""/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
119 </conditional>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
120 </xml>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
121
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
122 <xml name="inputs_copy_number_class_file_conditional">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
123 <conditional name="copy_number_conditional">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
124 <param argument="--copy_number" checked="false" label="Supplement Y matrix with copy number events" name="copy_number" type="boolean" truevalue="--copy_number" falsevalue=""/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
125 <when value="--copy_number">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
126 <expand macro="inputs_copy_number_class_file" />
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
127 </when>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
128 <when value=""/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
129 </conditional>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
130 </xml>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
131
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
132 <token name="@INPUTS_COPY_NUMBER_FILE_PREFIX@"><![CDATA[
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
133 #set $copy_number_conditional = type('',(object,),{'filename_copy_loss':$filename_copy_loss,'filename_copy_gain':$filename_copy_gain})()
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
134 ]]>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
135 </token>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
136
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
137 <token name="@INPUTS_COPY_NUMBER_FILE@"><![CDATA[
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
138 #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
139 --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
140 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
141 #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
142 --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
143 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
144 ]]>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
145 </token>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
146
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
147 <token name="@INPUTS_COPY_NUMBER_FILE_CONDITIONAL@"><![CDATA[
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
148 #if $copy_number_conditional.copy_number
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
149 $copy_number_conditional.copy_number
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
150 #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
151 --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
152 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
153 #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
154 --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
155 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
156 ##@INPUTS_COPY_NUMBER_FILE@
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
157 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
158 ]]>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
159 </token>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
160
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
161 <token name="@INPUTS_COPY_NUMBER_CLASS_FILE_PREFIX@"><![CDATA[
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
162 #set $copy_number_conditional = type('',(object,),{'filename_copy_loss':$filename_copy_loss,'filename_copy_gain':$filename_copy_gain,'filename_cancer_gene_classification':$filename_cancer_gene_classification})()
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
163 ]]>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
164 </token>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
165
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
166 <token name="@INPUTS_COPY_NUMBER_CLASS_FILE@"><![CDATA[
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
167 #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
168 --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
169 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
170 #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
171 --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
172 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
173 #if $copy_number_conditional.filename_cancer_gene_classification and $copy_number_conditional.filename_cancer_gene_classification is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
174 --filename_cancer_gene_classification '$copy_number_conditional.filename_cancer_gene_classification'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
175 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
176 ]]>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
177 </token>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
178
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
179 <token name="@INPUTS_COPY_NUMBER_CLASS_FILE_CONDITIONAL@"><![CDATA[
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
180 #if $copy_number_conditional.copy_number
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
181 $copy_number_conditional.copy_number
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
182 ##
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
183 #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
184 --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
185 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
186 #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
187 --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
188 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
189 #if $copy_number_conditional.filename_cancer_gene_classification and $copy_number_conditional.filename_cancer_gene_classification is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
190 --filename_cancer_gene_classification '$copy_number_conditional.filename_cancer_gene_classification'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
191 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
192 ##@INPUTS_COPY_NUMBER_CLASS_FILE@
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
193 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
194 ]]>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
195 </token>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
196
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
197 <xml name="input_remove_hyper">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
198 <param argument="--remove_hyper" checked="false" label="Remove hypermutated samples" name="remove_hyper" type="boolean" truevalue="--remove_hyper" falsevalue=""/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
199 </xml>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
200 <token name="@INPUT_REMOVE_HYPER@"><![CDATA[$remove_hyper]]></token>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
201
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
202 <xml name="input_alphas">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
203 <param argument="--alphas" label="the alphas for parameter sweep" name="alphas" optional="true" type="text" value="0.1,0.13,0.15,0.18,0.2,0.3,0.4,0.6,0.7"/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
204 </xml>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
205
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
206 <token name="@INPUTS_ALPHAS@"><![CDATA[
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
207 #if $alphas and $alphas is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
208 --alphas '$alphas'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
209 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
210 ]]>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
211 </token>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
212
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
213 <xml name="input_l1_ratios">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
214 <param argument="--l1_ratios" label="the l1 ratios for parameter sweep" name="l1_ratios" optional="true" type="text" value="0.1,0.125,0.15,0.2,0.25,0.3,0.35"/>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
215 </xml>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
216
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
217 <token name="@INPUTS_L1_RATIOS@"><![CDATA[
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
218 #if $l1_ratios and $l1_ratios is not None:
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
219 --l1_ratios '$l1_ratios'
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
220 #end if
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
221 ]]>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
222 </token>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
223 <xml name="citations">
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
224 <citations>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
225 <yield />
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
226 </citations>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
227 </xml>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
228 </macros>
3543d3e66ecb "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
parents:
diff changeset
229