Mercurial > repos > vijay > pancancer_apply_weights

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

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"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
author vijay
date Wed, 16 Dec 2020 23:30:39 +0000
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-1:000000000000 0:3543d3e66ecb
1 <macros>
2 <token name="@VERSION@">0.1.9</token>
3
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="@VERSION@">papaa</requirement>
7 </requirements>
8 </xml>
9
10 <xml name="stdio">
11 <stdio>
12 <exit_code level="fatal" range="1:"/>
13 </stdio>
14 </xml>
15
16 <xml name="inputs_basic">
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"/>
18 <yield/>
19 <param argument="--filename_mut" label="Filename mutations" name="filename_mut" optional="true" type="data" format="tabular" help="data/pancan_mutation_freeze.tsv.gz"/>
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"/>
21 <param argument="--filename_sample" label="Filename of sample" name="filename_sample" optional="true" type="data" format="tabular" help="data/sample_freeze.tsv"/>
22 </xml>
23
24 <token name="@INPUTS_BASIC@"><![CDATA[
25 #if $x_matrix and $x_matrix is not None:
26 --x_matrix '$x_matrix'
27 #end if
28 #if $filename_mut and $filename_mut is not None:
29 --filename_mut '$filename_mut'
30 #end if
31 #if $filename_mut_burden and $filename_mut_burden is not None:
32 --filename_mut_burden '$filename_mut_burden'
33 #end if
34 #if $filename_sample and $filename_sample is not None:
35 --filename_sample '$filename_sample'
36 #end if
37 ]]>
38 </token>
39
40 <xml name="inputs_genes_diseases">
41 <param argument="--genes" label="Comma separated string of HUGO gene symbols" name="genes" optional="False" type="text" value="ERBB2,PIK3CA,KRAS,AKT1"/>
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"/>
43 </xml>
44
45 <token name="@INPUTS_GENES_DISEASES@"><![CDATA[
46 #if $genes and $genes is not None:
47 --genes '$genes'
48 #end if
49 #if $diseases and str($diseases) != '':
50 --diseases '$diseases'
51 #end if
52 ]]>
53 </token>
54
55
56 <xml name="input_filename_raw_mut">
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"/>
58 </xml>
59
60 <token name="@INPUT_FILENAME_RAW_MUT@"><![CDATA[
61 #if $filename_raw_mut and $filename_raw_mut is not None:
62 --filename_raw_mut '$filename_raw_mut'
63 #end if
64 ]]>
65 </token>
66
67
68 <xml name="input_filename_burden">
69 <param argument="--filename_burden" label="Burden file" name="filename_burden" optional="true" type="data" format="tabular" help="data/seg_based_scores.tsv"/>
70 </xml>
71
72 <token name="@INPUT_FILENAME_BURDEN@"><![CDATA[
73 #if $filename_burden and $filename_burden is not None:
74 --filename_burden '$filename_burden'
75 #end if
76 ]]>
77 </token>
78
79 <xml name="input_filename_snaptron_samples">
80 <param argument="--sample_file" label="SNAPTRON samples" name="sample_file" optional="true" type="data" format="tabular" help="scripts/snaptron/samples.tsv.gz"/>
81 </xml>
82
83 <token name="@INPUT_FILENAME_SNAPTRON_SAMPLES@"><![CDATA[
84 #if $sample_file and $sample_file is not None:
85 --sample_file '$sample_file'
86 #end if
87 ]]>
88 </token>
89
90
91 <xml name="input_filename_snaptron_junctions">
92 <param argument="--junction_file" label="SNAPTRON junctions" name="junction_file" optional="true" type="data" format="tabular" help="scripts/snaptron/tp53_junctions.txt.gz"/>
93 </xml>
94
95 <token name="@INPUT_FILENAME_SNAPTRON_JUNCTIONS@"><![CDATA[
96 #if $junction_file and $junction_file is not None:
97 --junction_file '$junction_file'
98 #end if
99 ]]>
100 </token>
101
102 <xml name="inputs_copy_number_file">
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"/>
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"/>
105 </xml>
106
107 <xml name="inputs_copy_number_class_file">
108 <expand macro="inputs_copy_number_file" />
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"/>
110 </xml>
111
112 <xml name="inputs_copy_number_file_conditional">
113 <conditional name="copy_number_conditional">
114 <param argument="--copy_number" checked="false" label="Supplement Y matrix with copy number events" name="copy_number" type="boolean" truevalue="--copy_number" falsevalue=""/>
115 <when value="--copy_number">
116 <expand macro="inputs_copy_number_file" />
117 </when>
118 <when value=""/>
119 </conditional>
120 </xml>
121
122 <xml name="inputs_copy_number_class_file_conditional">
123 <conditional name="copy_number_conditional">
124 <param argument="--copy_number" checked="false" label="Supplement Y matrix with copy number events" name="copy_number" type="boolean" truevalue="--copy_number" falsevalue=""/>
125 <when value="--copy_number">
126 <expand macro="inputs_copy_number_class_file" />
127 </when>
128 <when value=""/>
129 </conditional>
130 </xml>
131
132 <token name="@INPUTS_COPY_NUMBER_FILE_PREFIX@"><![CDATA[
133 #set $copy_number_conditional = type('',(object,),{'filename_copy_loss':$filename_copy_loss,'filename_copy_gain':$filename_copy_gain})()
134 ]]>
135 </token>
136
137 <token name="@INPUTS_COPY_NUMBER_FILE@"><![CDATA[
138 #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
139 --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
140 #end if
141 #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
142 --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
143 #end if
144 ]]>
145 </token>
146
147 <token name="@INPUTS_COPY_NUMBER_FILE_CONDITIONAL@"><![CDATA[
148 #if $copy_number_conditional.copy_number
149 $copy_number_conditional.copy_number
150 #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
151 --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
152 #end if
153 #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
154 --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
155 #end if
156 ##@INPUTS_COPY_NUMBER_FILE@
157 #end if
158 ]]>
159 </token>
160
161 <token name="@INPUTS_COPY_NUMBER_CLASS_FILE_PREFIX@"><![CDATA[
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})()
163 ]]>
164 </token>
165
166 <token name="@INPUTS_COPY_NUMBER_CLASS_FILE@"><![CDATA[
167 #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
168 --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
169 #end if
170 #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
171 --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
172 #end if
173 #if $copy_number_conditional.filename_cancer_gene_classification and $copy_number_conditional.filename_cancer_gene_classification is not None:
174 --filename_cancer_gene_classification '$copy_number_conditional.filename_cancer_gene_classification'
175 #end if
176 ]]>
177 </token>
178
179 <token name="@INPUTS_COPY_NUMBER_CLASS_FILE_CONDITIONAL@"><![CDATA[
180 #if $copy_number_conditional.copy_number
181 $copy_number_conditional.copy_number
182 ##
183 #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
184 --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
185 #end if
186 #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
187 --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
188 #end if
189 #if $copy_number_conditional.filename_cancer_gene_classification and $copy_number_conditional.filename_cancer_gene_classification is not None:
190 --filename_cancer_gene_classification '$copy_number_conditional.filename_cancer_gene_classification'
191 #end if
192 ##@INPUTS_COPY_NUMBER_CLASS_FILE@
193 #end if
194 ]]>
195 </token>
196
197 <xml name="input_remove_hyper">
198 <param argument="--remove_hyper" checked="false" label="Remove hypermutated samples" name="remove_hyper" type="boolean" truevalue="--remove_hyper" falsevalue=""/>
199 </xml>
200 <token name="@INPUT_REMOVE_HYPER@"><![CDATA[$remove_hyper]]></token>
201
202 <xml name="input_alphas">
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"/>
204 </xml>
205
206 <token name="@INPUTS_ALPHAS@"><![CDATA[
207 #if $alphas and $alphas is not None:
208 --alphas '$alphas'
209 #end if
210 ]]>
211 </token>
212
213 <xml name="input_l1_ratios">
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"/>
215 </xml>
216
217 <token name="@INPUTS_L1_RATIOS@"><![CDATA[
218 #if $l1_ratios and $l1_ratios is not None:
219 --l1_ratios '$l1_ratios'
220 #end if
221 ]]>
222 </token>
223 <xml name="citations">
224 <citations>
225 <yield />
226 </citations>
227 </xml>
228 </macros>
229