annotate sRNAPipe.xml @ 1:1df6aaac800e draft

Deleted selected files
author brasset_jensen
date Wed, 13 Dec 2017 10:40:50 -0500
parents e4e71401c577
children cbd6577652a5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
1 <tool id="sRNAPipe" name="sRNAPipe" version="0.0.1">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
2 <description>In-depth study of small RNA</description>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
3 <command interpreter="perl">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
4
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
5 ./bin/sRNAPipe.pl
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
6
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
7 --fastq ${first_input}
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
8 --fastq_n ${first_input.name}
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
9 #for $input_file in $input_files:
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
10 --fastq ${input_file.additional_input}
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
11 --fastq_n ${input_file.additional_input.name}
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
12 #end for
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
13
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
14 #if $Genome.refGenomeSource == "history":
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
15 --ref "${Genome.ownFile}"
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
16 --build_index
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
17 #else:
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
18 --ref "${Genome.indices.fields.path}"
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
19 #end if
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
20
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
21 #if $tRNAs.refGenomeSource == "history":
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
22 --tRNAs "${tRNAs.ownFile}"
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
23 --build_tRNAs
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
24 #else:
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
25 --tRNAs "${tRNAs.indices.fields.path}"
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
26 #end if
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
27
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
28 #if $snRNAs.refGenomeSource == "history":
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
29 --snRNAs "${snRNAs.ownFile}"
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
30 --build_snRNAs
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
31 #else:
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
32 --snRNAs "${snRNAs.indices.fields.path}"
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
33 #end if
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
34
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
35 #if $miRNAs.refGenomeSource == "history":
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
36 --miRNAs "${miRNAs.ownFile}"
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
37 --build_miRNAs
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
38 #else:
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
39 --miRNAs "${miRNAs.indices.fields.path}"
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
40 #end if
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
41
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
42 #if $transcripts.refGenomeSource == "history":
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
43 --transcripts "${transcripts.ownFile}"
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
44 --build_transcripts
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
45 #else:
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
46 --transcripts "${transcripts.indices.fields.path}"
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
47 #end if
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
48
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
49 #if $TE.refGenomeSource == "history":
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
50 --TE "${TE.ownFile}"
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
51 --build_TE
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
52 #else:
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
53 --TE "${TE.indices.fields.path}"
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
54 #end if
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
55
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
56 #if $rRNAs.refGenomeSource == "history":
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
57 --rRNAs "${rRNAs.ownFile}"
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
58 --build_rRNAs
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
59 #else:
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
60 --rRNAs "${rRNAs.indices.fields.path}"
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
61 #end if
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
62
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
63 --si_min $si_min
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
64 --si_max $si_max
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
65 --pi_min $pi_min
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
66 --pi_max $pi_max
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
67 --min $min
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
68 --max $max
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
69
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
70 --mis $mis
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
71 --misTE $misTE
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
72 --dir $html_out.files_path
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
73 --html $html_out
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
74 --PPPon $PPPon
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
75 </command>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
76
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
77 <requirements>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
78 <requirement type="package" version="0.7.15">bwa</requirement>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
79 <requirement type="package" version="2.26.0">bedtools</requirement>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
80 <requirement type="package" version="1.5">samtools</requirement>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
81 </requirements>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
82
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
83 <inputs>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
84 <param format="fastqsanger" name="first_input" type="data" label="fastqsanger (Q33)" help=""/>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
85 <repeat name="input_files" title="Additional Fastq Files">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
86 <param format="fastqsanger" name="additional_input" type="data" label="fastqsanger (Q33)" help=""/>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
87 </repeat>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
88 <conditional name="Genome">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
89 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
90 <option value="indexed">Use a built-in index</option>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
91 <option value="history">Use one from the history</option>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
92 </param>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
93 <when value="indexed">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
94 <param name="indices" type="select" label="Select a reference genome">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
95 <options from_data_table="bwa_indexes">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
96 <filter type="sort_by" column="2" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
97 <validator type="no_options" message="No indexes are available" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
98 </options>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
99 </param>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
100 </when>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
101 <when value="history">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
102 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
103 </when>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
104 </conditional>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
105 <conditional name="TE">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
106 <param name="refGenomeSource" type="select" label="Will you select TE database from your history or use a built-in index?">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
107 <option value="indexed">Use a built-in index</option>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
108 <option value="history">Use one from the history</option>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
109 </param>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
110 <when value="indexed">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
111 <param name="indices" type="select" label="Select a TE reference">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
112 <options from_data_table="bwa_indexes">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
113 <filter type="sort_by" column="2" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
114 <validator type="no_options" message="No indexes are available" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
115 </options>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
116 </param>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
117 </when>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
118 <when value="history">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
119 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
120 </when>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
121 </conditional>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
122 <conditional name="miRNAs">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
123 <param name="refGenomeSource" type="select" label="Will you select miRNA database from your history or use a built-in index?">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
124 <option value="indexed">Use a built-in index</option>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
125 <option value="history">Use one from the history</option>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
126 </param>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
127 <when value="indexed">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
128 <param name="indices" type="select" label="Select a miRNA reference">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
129 <options from_data_table="bwa_indexes">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
130 <filter type="sort_by" column="2" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
131 <validator type="no_options" message="No indexes are available" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
132 </options>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
133 </param>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
134 </when>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
135 <when value="history">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
136 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
137 </when>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
138 </conditional>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
139 <conditional name="snRNAs">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
140 <param name="refGenomeSource" type="select" label="Will you select snRNA database from your history or use a built-in index?">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
141 <option value="indexed">Use a built-in index</option>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
142 <option value="history">Use one from the history</option>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
143 </param>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
144 <when value="indexed">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
145 <param name="indices" type="select" label="Select a snRNAs reference">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
146 <options from_data_table="bwa_indexes">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
147 <filter type="sort_by" column="2" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
148 <validator type="no_options" message="No indexes are available" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
149 </options>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
150 </param>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
151 </when>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
152 <when value="history">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
153 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
154 </when>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
155 </conditional>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
156 <conditional name="rRNAs">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
157 <param name="refGenomeSource" type="select" label="Will you select rRNAs database from your history or use a built-in index?">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
158 <option value="indexed">Use a built-in index</option>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
159 <option value="history">Use one from the history</option>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
160 </param>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
161 <when value="indexed">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
162 <param name="indices" type="select" label="Select a rRNAs reference">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
163 <options from_data_table="bwa_indexes">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
164 <filter type="sort_by" column="2" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
165 <validator type="no_options" message="No indexes are available" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
166 </options>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
167 </param>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
168 </when>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
169 <when value="history">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
170 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
171 </when>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
172 </conditional>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
173 <conditional name="tRNAs">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
174 <param name="refGenomeSource" type="select" label="Will you select tRNA database from your history or use a built-in index?">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
175 <option value="indexed">Use a built-in index</option>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
176 <option value="history">Use one from the history</option>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
177 </param>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
178 <when value="indexed">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
179 <param name="indices" type="select" label="Select a tRNA reference">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
180 <options from_data_table="bwa_indexes">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
181 <filter type="sort_by" column="2" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
182 <validator type="no_options" message="No indexes are available" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
183 </options>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
184 </param>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
185 </when>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
186 <when value="history">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
187 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
188 </when>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
189 </conditional>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
190 <conditional name="transcripts">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
191 <param name="refGenomeSource" type="select" label="Will you select transcripts database from your history or use a built-in index?">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
192 <option value="indexed">Use a built-in index</option>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
193 <option value="history">Use one from the history</option>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
194 </param>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
195 <when value="indexed">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
196 <param name="indices" type="select" label="Select a transcripts reference">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
197 <options from_data_table="bwa_indexes">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
198 <filter type="sort_by" column="2" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
199 <validator type="no_options" message="No indexes are available" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
200 </options>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
201 </param>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
202 </when>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
203 <when value="history">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
204 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
205 </when>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
206 </conditional>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
207 <param name="min" type="integer" value="18" label="minimum read size"/>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
208 <param name="max" type="integer" value="29" label="maximum read size"/>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
209 <param name="si_min" type="integer" value="21" label="lower bound of siRNA range"/>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
210 <param name="si_max" type="integer" value="21" label="higher bound of siRNA range"/>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
211 <param name="pi_min" type="integer" value="23" label="lower bound of piRNA range"/>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
212 <param name="pi_max" type="integer" value="29" label="higher bound of piRNA range"/>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
213
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
214 <param name="mis" type="integer" value="0" label="maximal genome mismatches"/>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
215 <param name="misTE" type="integer" value="3" label="maximal TE mismatches"/>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
216 <param name="PPPon" type="boolean" checked="true" label="PPPartners"/>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
217 </inputs>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
218 <outputs>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
219 <data format="html" name="html_out" label="${tool.name}_${first_input.name}_${on_string}"/>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
220
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
221 <collection format ="fastqsanger" type="list" label="${tool.name}_fastq_outputs" name="output_fastqsanger">
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
222 <discover_datasets format ="fastqsanger" pattern="(?P&lt;name&gt;.*)" directory="fastq_dir" />
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
223 </collection>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
224
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
225 </outputs>
e4e71401c577 Uploaded
brasset_jensen
parents:
diff changeset
226 </tool>