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comparison paralyzer.xml @ 1:f880686a9194 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
author rnateam
date Wed, 23 Oct 2019 19:07:22 -0400
parents 4dbe81be8b81
children
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0:4dbe81be8b81 1:f880686a9194
1 <tool id="paralyzer" name="PARalyzer" version="1.5"> 1 <tool id="paralyzer" name="PARalyzer" version="1.5">
2
3 <description>A method to map interaction sites between RNA-binding proteins 2 <description>A method to map interaction sites between RNA-binding proteins
4 and their targets</description> 3 and their targets</description>
5
6 <requirements> 4 <requirements>
7 <!-- conda dependency --> 5 <!-- conda dependency -->
8 <requirement type="package" version="1.5">paralyzer</requirement> 6 <requirement type="package" version="1.5">paralyzer</requirement>
9 <requirement type="package" version="324">ucsc-fatotwobit</requirement> 7 <requirement type="package" version="324">ucsc-fatotwobit</requirement>
10 </requirements> 8 </requirements>
11 9 <command detect_errors="aggressive"><![CDATA[
12 <command> 10
13 <![CDATA[
14 #if $refGenomeSource.genomeSource == "history": 11 #if $refGenomeSource.genomeSource == "history":
15 faToTwoBit '$refGenomeSource.ownFile' ownFile.2bit 12 faToTwoBit '$refGenomeSource.ownFile' ownFile.2bit
16 && 13 &&
17 #end if 14 #end if
18 15
22 ## <env id="_JAVA_OPTIONS">-Xmx12G</env> 19 ## <env id="_JAVA_OPTIONS">-Xmx12G</env>
23 PARalyzer 2G $input_ini 20 PARalyzer 2G $input_ini
24 21
25 ]]> 22 ]]>
26 </command> 23 </command>
24 <configfiles>
25 <configfile name="input_ini">
26 ## genome source
27 #if $refGenomeSource.genomeSource == "history":
28 GENOME_2BIT_FILE=ownFile.2bit
29 #else
30 GENOME_2BIT_FILE=$refGenomeSource.builtin.fields.path
31 #end if
32
33 SAM_FILE=$input_sam$collapse
34
35 #if $methods.choice == "ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL":
36 ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL=$methods.max_num
37 #else:
38 $methods.choice
39 #end if
40
41 #if $conversion.selection == "custom":
42 CONVERSION=$conversion.character_from>$conversion.character_to
43 #end if
44
45 ## required parameters
46 #if $params.settingsType == "custom":
47 BANDWIDTH=$params.BANDWIDTH
48 MINIMUM_READ_COUNT_PER_GROUP=$params.min_read_group
49 MINIMUM_READ_COUNT_PER_CLUSTER=$params.min_read_cluster
50 MINIMUM_READ_COUNT_FOR_KDE=$params.min_read_kde
51 MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=$params.min_read_cluster_inc
52 MINIMUM_CLUSTER_SIZE=$params.min_cluster_size
53 MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=$params.min_conv_loc_cluster
54 MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=$params.min_conv_cluster
55 MINIMUM_READ_LENGTH=$params.min_read_len
56 MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=$params.max_num_conv_mis
57 #end if
58
59 OUTPUT_DISTRIBUTIONS_FILE=out.distribution
60 OUTPUT_GROUPS_FILE=out.groups
61 OUTPUT_CLUSTERS_FILE=out.clusters
62 </configfile>
63 </configfiles>
27 <inputs> 64 <inputs>
28 <param name="input_sam" type="data" 65 <param name="input_sam" type="data"
29 format="sam" label="Alignment" 66 format="sam" label="Alignment"
30 help="The sam file containing alignment of the read data."/> 67 help="The sam file containing alignment of the read data."/>
31 68
205 message="Minimum allowed value is 1" min="1"/> 242 message="Minimum allowed value is 1" min="1"/>
206 </param> 243 </param>
207 </when> <!-- full --> 244 </when> <!-- full -->
208 </conditional> 245 </conditional>
209 </inputs> 246 </inputs>
210 <configfiles>
211 <configfile name="input_ini">
212 ## genome source
213 #if $refGenomeSource.genomeSource == "history":
214 GENOME_2BIT_FILE=ownFile.2bit
215 #else
216 GENOME_2BIT_FILE=$refGenomeSource.builtin.fields.path
217 #end if
218
219 SAM_FILE=$input_sam$collapse
220
221 #if $methods.choice == "ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL":
222 ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL=$methods.max_num
223 #else:
224 $methods.choice
225 #end if
226
227 #if $conversion.selection == "custom":
228 CONVERSION=$conversion.character_from>$conversion.character_to
229 #end if
230
231 ## required parameters
232 #if $params.settingsType == "custom":
233 BANDWIDTH=$params.BANDWIDTH
234 MINIMUM_READ_COUNT_PER_GROUP=$params.min_read_group
235 MINIMUM_READ_COUNT_PER_CLUSTER=$params.min_read_cluster
236 MINIMUM_READ_COUNT_FOR_KDE=$params.min_read_kde
237 MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=$params.min_read_cluster_inc
238 MINIMUM_CLUSTER_SIZE=$params.min_cluster_size
239 MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=$params.min_conv_loc_cluster
240 MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=$params.min_conv_cluster
241 MINIMUM_READ_LENGTH=$params.min_read_len
242 MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=$params.max_num_conv_mis
243 #end if
244
245 OUTPUT_DISTRIBUTIONS_FILE=out.distribution
246 OUTPUT_GROUPS_FILE=out.groups
247 OUTPUT_CLUSTERS_FILE=out.clusters
248 </configfile>
249 </configfiles>
250 <outputs> 247 <outputs>
251 <data name="distribution" format="txt" 248 <data name="distribution" format="txt"
252 from_work_dir="out.distribution" 249 from_work_dir="out.distribution"
253 label="${tool.name} on ${on_string}: DISTRIBUTIONS"/> 250 label="${tool.name} on ${on_string}: DISTRIBUTIONS"/>
254 251