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comparison sRNAPipe.xml @ 4:bf3c8bf8b819 draft

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author romaingred
date Wed, 13 Dec 2017 10:24:17 -0500
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3:e9c9cee888cf 4:bf3c8bf8b819
1 <tool id="sRNAPipe" name="sRNAPipe" version="0.0.1">
2 <description>Full study of sRNA</description>
3 <command interpreter="perl">
4
5 ./bin/sRNAPipe.pl
6
7 --fastq ${first_input}
8 --fastq_n ${first_input.name}
9 #for $input_file in $input_files:
10 --fastq ${input_file.additional_input}
11 --fastq_n ${input_file.additional_input.name}
12 #end for
13
14 #if $Genome.refGenomeSource == "history":
15 --ref "${Genome.ownFile}"
16 --build_index
17 #else:
18 --ref "${Genome.indices.fields.path}"
19 #end if
20
21 #if $tRNAs.refGenomeSource == "history":
22 --tRNAs "${tRNAs.ownFile}"
23 --build_tRNAs
24 #else:
25 --tRNAs "${tRNAs.indices.fields.path}"
26 #end if
27
28 #if $snRNAs.refGenomeSource == "history":
29 --snRNAs "${snRNAs.ownFile}"
30 --build_snRNAs
31 #else:
32 --snRNAs "${snRNAs.indices.fields.path}"
33 #end if
34
35 #if $miRNAs.refGenomeSource == "history":
36 --miRNAs "${miRNAs.ownFile}"
37 --build_miRNAs
38 #else:
39 --miRNAs "${miRNAs.indices.fields.path}"
40 #end if
41
42 #if $transcripts.refGenomeSource == "history":
43 --transcripts "${transcripts.ownFile}"
44 --build_transcripts
45 #else:
46 --transcripts "${transcripts.indices.fields.path}"
47 #end if
48
49 #if $TE.refGenomeSource == "history":
50 --TE "${TE.ownFile}"
51 --build_TE
52 #else:
53 --TE "${TE.indices.fields.path}"
54 #end if
55
56 #if $rRNAs.refGenomeSource == "history":
57 --rRNAs "${rRNAs.ownFile}"
58 --build_rRNAs
59 #else:
60 --rRNAs "${rRNAs.indices.fields.path}"
61 #end if
62
63 --si_min $si_min
64 --si_max $si_max
65 --pi_min $pi_min
66 --pi_max $pi_max
67 --min $min
68 --max $max
69
70 --mis $mis
71 --misTE $misTE
72 --dir $html_out.files_path
73 --html $html_out
74 --PPPon $PPPon
75 </command>
76
77 <requirements>
78 <requirement type="package" version="0.7.15">bwa</requirement>
79 <requirement type="package" version="2.26.0">bedtools</requirement>
80 <requirement type="package" version="1.5">samtools</requirement>
81 </requirements>
82
83 <inputs>
84 <param format="fastqsanger" name="first_input" type="data" label="fastqsanger (Q33)" help=""/>
85 <repeat name="input_files" title="Additional Fastq Files">
86 <param format="fastqsanger" name="additional_input" type="data" label="fastqsanger (Q33)" help=""/>
87 </repeat>
88 <conditional name="Genome">
89 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
90 <option value="indexed">Use a built-in index</option>
91 <option value="history">Use one from the history</option>
92 </param>
93 <when value="indexed">
94 <param name="indices" type="select" label="Select a reference genome">
95 <options from_data_table="bwa_indexes">
96 <filter type="sort_by" column="2" />
97 <validator type="no_options" message="No indexes are available" />
98 </options>
99 </param>
100 </when>
101 <when value="history">
102 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
103 </when>
104 </conditional>
105 <conditional name="TE">
106 <param name="refGenomeSource" type="select" label="Will you select TE database from your history or use a built-in index?">
107 <option value="indexed">Use a built-in index</option>
108 <option value="history">Use one from the history</option>
109 </param>
110 <when value="indexed">
111 <param name="indices" type="select" label="Select a TE reference">
112 <options from_data_table="bwa_indexes">
113 <filter type="sort_by" column="2" />
114 <validator type="no_options" message="No indexes are available" />
115 </options>
116 </param>
117 </when>
118 <when value="history">
119 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
120 </when>
121 </conditional>
122 <conditional name="miRNAs">
123 <param name="refGenomeSource" type="select" label="Will you select miRNA database from your history or use a built-in index?">
124 <option value="indexed">Use a built-in index</option>
125 <option value="history">Use one from the history</option>
126 </param>
127 <when value="indexed">
128 <param name="indices" type="select" label="Select a miRNA reference">
129 <options from_data_table="bwa_indexes">
130 <filter type="sort_by" column="2" />
131 <validator type="no_options" message="No indexes are available" />
132 </options>
133 </param>
134 </when>
135 <when value="history">
136 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
137 </when>
138 </conditional>
139 <conditional name="snRNAs">
140 <param name="refGenomeSource" type="select" label="Will you select snRNA database from your history or use a built-in index?">
141 <option value="indexed">Use a built-in index</option>
142 <option value="history">Use one from the history</option>
143 </param>
144 <when value="indexed">
145 <param name="indices" type="select" label="Select a snRNAs reference">
146 <options from_data_table="bwa_indexes">
147 <filter type="sort_by" column="2" />
148 <validator type="no_options" message="No indexes are available" />
149 </options>
150 </param>
151 </when>
152 <when value="history">
153 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
154 </when>
155 </conditional>
156 <conditional name="rRNAs">
157 <param name="refGenomeSource" type="select" label="Will you select rRNAs database from your history or use a built-in index?">
158 <option value="indexed">Use a built-in index</option>
159 <option value="history">Use one from the history</option>
160 </param>
161 <when value="indexed">
162 <param name="indices" type="select" label="Select a rRNAs reference">
163 <options from_data_table="bwa_indexes">
164 <filter type="sort_by" column="2" />
165 <validator type="no_options" message="No indexes are available" />
166 </options>
167 </param>
168 </when>
169 <when value="history">
170 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
171 </when>
172 </conditional>
173 <conditional name="tRNAs">
174 <param name="refGenomeSource" type="select" label="Will you select tRNA database from your history or use a built-in index?">
175 <option value="indexed">Use a built-in index</option>
176 <option value="history">Use one from the history</option>
177 </param>
178 <when value="indexed">
179 <param name="indices" type="select" label="Select a tRNA reference">
180 <options from_data_table="bwa_indexes">
181 <filter type="sort_by" column="2" />
182 <validator type="no_options" message="No indexes are available" />
183 </options>
184 </param>
185 </when>
186 <when value="history">
187 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
188 </when>
189 </conditional>
190 <conditional name="transcripts">
191 <param name="refGenomeSource" type="select" label="Will you select transcripts database from your history or use a built-in index?">
192 <option value="indexed">Use a built-in index</option>
193 <option value="history">Use one from the history</option>
194 </param>
195 <when value="indexed">
196 <param name="indices" type="select" label="Select a transcripts reference">
197 <options from_data_table="bwa_indexes">
198 <filter type="sort_by" column="2" />
199 <validator type="no_options" message="No indexes are available" />
200 </options>
201 </param>
202 </when>
203 <when value="history">
204 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
205 </when>
206 </conditional>
207 <param name="min" type="integer" value="18" label="minimum read size"/>
208 <param name="max" type="integer" value="29" label="maximum read size"/>
209 <param name="si_min" type="integer" value="21" label="lower bound of siRNA range"/>
210 <param name="si_max" type="integer" value="21" label="higher bound of siRNA range"/>
211 <param name="pi_min" type="integer" value="23" label="lower bound of piRNA range"/>
212 <param name="pi_max" type="integer" value="29" label="higher bound of piRNA range"/>
213
214 <param name="mis" type="integer" value="0" label="maximal genome mismatches"/>
215 <param name="misTE" type="integer" value="3" label="maximal TE mismatches"/>
216 <param name="PPPon" type="boolean" checked="true" label="PPPartners"/>
217 </inputs>
218 <outputs>
219 <data format="html" name="html_out" label="${tool.name}_${first_input.name}_${on_string}"/>
220
221 <collection format ="fastqsanger" type="list" label="${tool.name}_fastq_outputs" name="output_fastqsanger">
222 <discover_datasets format ="fastqsanger" pattern="(?P&lt;name&gt;.*)" directory="fastq_dir" />
223 </collection>
224
225 </outputs>
226 </tool>