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comparison sRNAPipe.xml @ 69:fa794d2a5aaf draft

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planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit bd03f99240a3d174c1b22245fbdf45e15edb4a5e
author brasset_jensen
date Tue, 12 Feb 2019 04:11:07 -0500
parents 740884893563
children be25d16676f6
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68:a5a99218ef7a 69:fa794d2a5aaf
1 <tool id="sRNAPipe" name="sRNAPipe" version="1.1"> 1 <tool id="sRNAPipe" name="sRNAPipe" version="1.1">
2 <description>In-depth study of small RNA</description> 2 <description>In-depth study of small RNA</description>
3 <macros> 3 <macros>
4 <xml name="source" token_arg="Argument" token_build="Build argument"> 4 <xml name="source" token_arg="Argument" token_build="Build argument" token_ref="">
5 <conditional name="source"> 5 <conditional name="source">
6 <param name="source" type="select" label="Will you select the database from your history or use a built-in index?"> 6 <param name="source" type="select" label="Will you select the reference database from your history or use a built-in index?">
7 <option value="indexed">Use a built-in index</option> 7 <option value="indexed">Use a built-in index</option>
8 <option value="history">Use one from the history</option> 8 <option value="history">Use one from the history</option>
9 </param> 9 </param>
10 <when value="indexed"> 10 <when value="indexed">
11 <param name="indices" argument="@ARG@" type="select" label="Select a reference genome" help="Also use @BUILD@"> 11 <param name="indices" argument="@ARG@" type="select" label="Select @REF@">
12 <options from_data_table="bwa_indexes"> 12 <options from_data_table="bwa_indexes">
13 <filter type="sort_by" column="2" /> 13 <filter type="sort_by" column="2" />
14 <validator type="no_options" message="No indexes are available" /> 14 <validator type="no_options" message="No indexes are available" />
15 </options> 15 </options>
16 </param> 16 </param>
17 </when> 17 </when>
18 <when value="history"> 18 <when value="history">
19 <param name="file" argument="@ARG@" type="data" format="fasta" label="Select a reference from history" /> 19 <param name="file" argument="@ARG@" type="data" format="fasta" label="Select @REF@ from history" help="We will also use @BUILD@"/>
20 </when> 20 </when>
21 </conditional>
22 </xml>
23 <xml name="conditional_source" token_arg="Argument" token_build="Build argument" token_ref="" token_name="">
24 <conditional name="@NAME@">
25 <param name="use_ref" type="select" label="Use @REF@?">
26 <option value="true">Yes</option>
27 <option value="false" selected="true">No</option>
28 </param>
29 <when value="true">
30 <expand macro="source" arg="@ARG@" build="@BUILD@" ref="@REF@"/>
31 </when>
32 <when value="false"/>
21 </conditional> 33 </conditional>
22 </xml> 34 </xml>
23 </macros> 35 </macros>
24 <requirements> 36 <requirements>
25 <requirement type="package" version="1.1">srnapipe</requirement> 37 <requirement type="package" version="1.1">srnapipe</requirement>
26 </requirements> 38 </requirements>
27 <version_command>srnapipe | grep 'version' | grep "version" | cut -d ' ' -f 3</version_command> 39 <version_command>srnapipe | grep 'version' | grep "version" | cut -d ' ' -f 3</version_command>
28 <command detect_errors="aggressive"><![CDATA[ 40 <command detect_errors="aggressive"><![CDATA[
29 srnapipe 41 srnapipe
30 42 #if str($inputs.custom) == 'true'
31 --fastq '${first_input}' 43 #for $x in $inputs.inputs
32 --fastq_n '${first_input.name}' 44 --fastq '$x.fastq'
33 #for $input_file in $input_files: 45 --fastq_n '$x.fastq_n'
34 --fastq '${input_file.additional_input}'
35 --fastq_n '${input_file.additional_input.name}'
36 #end for 46 #end for
37 47 #else
38 #if $genome.source.source == "history": 48 #for $x in $inputs.fastq
39 --ref '${genome.source.file}' 49 --fastq '$x'
40 --build_index 50 --fastq_n '$x.element_identifier'
41 #else: 51 #end for
42 --ref '${genome.source.indices.fields.path}' 52 #end if
53 --min $min
54 --max $max
55
56 #if $genome.source.source == "history"
57 --ref '$genome.source.file'
58 --build_index
59 #else
60 --ref '$genome.source.indices.fields.path'
61 #end if
62 --mis $genome.mis
63
64 #if $transcripts.source.source == "history"
65 --transcripts '$transcripts.source.file'
66 --build_transcripts
67 #else
68 --transcripts '$transcripts.source.indices.fields.path'
69 #end if
70
71 #if $te.source.source == "history"
72 --TE '$te.source.file'
73 --build_TE
74 #else
75 --TE '$te.source.indices.fields.path'
76 #end if
77 --misTE $te.misTE
78
79 #if $mirnas.source.source == "history"
80 --miRNAs '$mirnas.source.file'
81 --build_miRNAs
82 #else:
83 --miRNAs '$mirnas.source.indices.fields.path'
84 #end if
85
86 #if str($snrnas.snrnas.use_ref) == 'true'
87 #if str($snrnas.snrnas.source.source) == "history"
88 --snRNAs '$snrnas.snrnas.source.file'
89 --build_snRNAs
90 #else
91 --snRNAs '$snrnas.snrnas.source.indices.fields.path'
43 #end if 92 #end if
44 93 #else
45 #if $tRNAs.source.source == "history": 94 --snRNAs "None"
46 --tRNAs '${tRNAs.source.file}' 95 #end if
47 --build_tRNAs 96
48 #elif $tRNAs.source.source == "none": 97 #if str($rrnas.rrnas.use_ref) == 'true'
49 --tRNAs "None" 98 #if str($rrnas.rrnas.source.source) == "history"
50 #else: 99 --rRNAs '$rrnas.rrnas.source.file'
51 --tRNAs '${tRNAs.source.indices.fields.path}' 100 --build_rRNAs
101 #else
102 --rRNAs '$rrnas.rrnas.source.indices.fields.path'
52 #end if 103 #end if
53 104 #else
54 #if $snRNAs.source.source == "history": 105 --rRNAs "None"
55 --snRNAs '${snRNAs.source.file}' 106 #end if
56 --build_snRNAs 107
57 #elif $snRNAs.source.source == "none": 108 #if str($trnas.trnas.use_ref) == 'true'
58 --snRNAs "None" 109 #if str($trnas.trnas.source.source) == "history"
59 #else: 110 --tRNAs '$trnas.trnas.source.file'
60 --snRNAs '${snRNAs.source.indices.fields.path}' 111 --build_tRNAs
112 #else
113 --tRNAs '$trnas.trnas.source.indices.fields.path'
61 #end if 114 #end if
62 115 #else
63 #if $rRNAs.source.source == "history": 116 --tRNAs "None"
64 --rRNAs '${rRNAs.source.file}' 117 #end if
65 --build_rRNAs 118
66 #elif $rRNAs.source.source == "none": 119 --si_min $sirna.si_min
67 --rRNAs "None" 120 --si_max $sirna.si_max
68 #else: 121 --pi_min $pirna.pi_min
69 --rRNAs '${rRNAs.source.indices.fields.path}' 122 --pi_max $pirna.pi_max
70 #end if 123 --dir $html_out.files_path
71 124 --html $html_out
72 #if $miRNAs.source.source == "history": 125 --PPPon $PPPon
73 --miRNAs '${miRNAs.source.file}'
74 --build_miRNAs
75 #else:
76 --miRNAs '${miRNAs.source.indices.fields.path}'
77 #end if
78
79 #if $transcripts.source.source == "history":
80 --transcripts '${transcripts.source.file}'
81 --build_transcripts
82 #else:
83 --transcripts '${transcripts.source.indices.fields.path}'
84 #end if
85
86 #if $TE.source.source == "history":
87 --TE '${TE.source.file}'
88 --build_TE
89 #else:
90 --TE '${TE.source.indices.fields.path}'
91 #end if
92
93 --si_min $si_min
94 --si_max $si_max
95 --pi_min $pi_min
96 --pi_max $pi_max
97 --min $min
98 --max $max
99
100 --mis $mis
101 --misTE $misTE
102 --dir $html_out.files_path
103 --html $html_out
104 --PPPon $PPPon
105 ]]> 126 ]]>
106 </command> 127 </command>
107
108 <inputs> 128 <inputs>
109 <param name="first_input" argument="--fastq" type="data" format="fastqsanger" label="fastqsanger (Q33)" help="Also set a name with --fastq_n"/> 129 <conditional name="inputs">
110 <repeat name="input_files" title="Additional Fastq Files"> 130 <param name="custom" type="select" label="Use custom name for the input sequence files?">
111 <param name="additional_input" argument="--fastq" type="data" format="fastqsanger" label="fastqsanger (Q33)" help="Also set a name after each fastq with --fastq_n"/> 131 <option value="true">Yes</option>
112 </repeat> 132 <option value="false" selected="true">No: the names will be extracted automatically</option>
133 </param>
134 <when value="true">
135 <repeat name="inputs" title="Input sequences" min="1">
136 <param argument="--fastq" type="data" format="fastqsanger" label="Input sequences"/>
137 <param argument="--fastq_n" type="text" value="" label="Label for the input sequences"/>
138 </repeat>
139 </when>
140 <when value="false">
141 <param argument="--fastq" type="data" format="fastqsanger" multiple="true" label="Input sequences" help="Also set a name with --fastq_n"/>
142 </when>
143 </conditional>
144 <param argument="--min" type="integer" value="18" label="Minimum read size"/>
145 <param argument="--max" type="integer" value="29" label="Maximum read size"/>
113 <section name="genome" title="Reference genome" expanded="true"> 146 <section name="genome" title="Reference genome" expanded="true">
114 <expand macro="source" arg="--ref" build="--build_index"/> 147 <expand macro="source" arg="--ref" build="--build_index" ref="a reference genome"/>
148 <param argument="--mis" type="integer" value="0" label="Maximal genome mismatches"/>
115 </section> 149 </section>
116 <section name="transcripts" title="Transcripts" expanded="true"> 150 <section name="transcripts" title="Transcripts" expanded="true">
117 <expand macro="source" arg="--transcripts" build="--build_transcripts"/> 151 <expand macro="source" arg="--transcripts" build="--build_transcripts" ref="reference transcript sequences"/>
118 </section> 152 </section>
119 <section name="TE" title="Transposable Elements" expanded="true"> 153 <section name="te" title="Transposable Elements" expanded="true">
120 <expand macro="source" arg="--TE" build="--build_TE"/> 154 <expand macro="source" arg="--TE" build="--build_TE" ref="reference TE sequences"/>
121 </section> 155 <param argument="--misTE" type="integer" value="3" label="maximal TE mismatches"/>
122 <section name="miRNAs" title="miRNAs" expanded="true"> 156 </section>
123 <expand macro="source" arg="--miRNAs" build="--build_miRNAs"/> 157 <section name="mirnas" title="miRNAs" expanded="true">
124 </section> 158 <expand macro="source" arg="--miRNAs" build="--build_miRNAs" ref="reference miRNAs sequences"/>
125 <section name="snRNAs" title="snRNAs" expanded="true"> 159 </section>
126 <expand macro="source" arg="--snRNAs" build="--build_snRNAs"/> 160 <section name="snrnas" title="snRNAs" expanded="true">
127 </section> 161 <expand macro="conditional_source" name="snrnas" arg="--snRNAs" build="--build_snRNAs" ref="reference snRNAs sequences"/>
128 <section name="rRNAs" title="rRNAs" expanded="true"> 162 </section>
129 <expand macro="source" arg="--rRNAs" build="--build_rRNAs"/> 163 <section name="rrnas" title="rRNAs" expanded="true">
130 </section> 164 <expand macro="conditional_source" name="rrnas" arg="--rRNAs" build="--build_rRNAs" ref="reference rRNAs sequences"/>
131 <section name="tRNAs" title="tRNAs" expanded="true"> 165 </section>
132 <expand macro="source" arg="--tRNAs" build="--build_tRNAs"/> 166 <section name="trnas" title="tRNAs" expanded="true">
133 </section> 167 <expand macro="conditional_source" name="trnas" arg="--tRNAs" build="--build_tRNAs" ref="reference tRNAs sequences"/>
134 168 </section>
135 <param name="min" argument="--min" type="integer" value="18" label="minimum read size"/> 169 <section name="sirna" title="siRNA" expanded="true">
136 <param name="max" argument="--max" type="integer" value="29" label="maximum read size"/> 170 <param argument="--si_min" type="integer" value="21" label="Lower bound for siRNA range"/>
137 <param name="si_min" argument="--si_min" type="integer" value="21" label="lower bound of siRNA range"/> 171 <param argument="--si_max" type="integer" value="21" label="Higher bound of siRNA range"/>
138 <param name="si_max" argument="--si_max" type="integer" value="21" label="higher bound of siRNA range"/> 172 </section>
139 <param name="pi_min" argument="--pi_min" type="integer" value="23" label="lower bound of piRNA range"/> 173 <section name="pirna" title="piRNA" expanded="true">
140 <param name="pi_max" argument="--pi_max" type="integer" value="29" label="higher bound of piRNA range"/> 174 <param argument="--pi_min" type="integer" value="23" label="lower bound of piRNA range"/>
141 <param name="mis" argument="--mis" type="integer" value="0" label="maximal genome mismatches"/> 175 <param argument="--pi_max" type="integer" value="29" label="higher bound of piRNA range"/>
142 <param name="misTE" argument="--misTE" type="integer" value="3" label="maximal TE mismatches"/> 176 </section>
143 <param name="PPPon" argument="--PPPon" type="boolean" checked="true" label="PPPartners"/> 177 <param name="PPPon" argument="--PPPon" type="boolean" truevalue="true" falsevalue="false" checked="true" label="PPPartners"/>
144 </inputs> 178 </inputs>
145 <outputs> 179 <outputs>
146 <data format="html" name="html_out" label="${tool.name} on ${first_input.name} (${on_string}): HTML report"/> 180 <data format="html" name="html_out" label="${tool.name} on ${on_string}: HTML report"/>
147 <collection type="list" label="${tool.name}_fastq_outputs" name="output_fastqsanger"> 181 <collection type="list" label="${tool.name} on ${on_string}: FastQ outputs" name="output_fastqsanger">
148 <discover_datasets format ="fastqsanger" pattern="__designation_and_ext__" directory="fastq_dir" /> 182 <discover_datasets format ="fastqsanger" pattern="__designation_and_ext__" directory="fastq_dir" />
149 </collection> 183 </collection>
150 </outputs> 184 </outputs>
151 <tests> 185 <tests>
152 <test> 186 <test>
153 <param name="first_input" value="reads-sample-small.fastq" /> 187 <conditional name="inputs">
154 <section name="genome"> 188 <param name="custom" value="false"/>
155 <conditional name="source"> 189 <param name="fastq" value="reads-sample-small.fastq"/>
156 <param name="source" value="history" /> 190 </conditional>
157 <param name="file" value ="genome-small.fa" />
158 </conditional>
159 </section>
160 <section name="transcripts">
161 <conditional name="source">
162 <param name="source" value="history" />
163 <param name="file" value ="transcripts-file-small.fa" />
164 </conditional>
165 </section>
166 <section name="TE">
167 <conditional name="source">
168 <param name="source" value="history" />
169 <param name="file" value ="TE-file-small.fa" />
170 </conditional>
171 </section>
172 <section name="miRNAs">
173 <conditional name="source">
174 <param name="source" value="history" />
175 <param name="file" value ="mirbase-21-dme-hairpins-16jul2015.fa" />
176 </conditional>
177 </section>
178 <section name="snRNAs">
179 <conditional name="source">
180 <param name="source" value="history" />
181 <param name="file" value ="dmel-all-sn-snoRNA-r6.03.fasta" />
182 </conditional>
183 </section>
184 <section name="rRNAs">
185 <conditional name="source">
186 <param name="source" value="history" />
187 <param name="file" value ="dmel-all-rRNA-r6.03.fasta" />
188 </conditional>
189 </section>
190 <section name="tRNAs">
191 <conditional name="source">
192 <param name="source" value="history" />
193 <param name="file" value ="dmel-all-tRNA-r6.03.fasta" />
194 </conditional>
195 </section>
196 <param name="min" value="18" /> 191 <param name="min" value="18" />
197 <param name="max" value="29" /> 192 <param name="max" value="29" />
198 <param name="si_min" value="21" /> 193 <section name="genome">
199 <param name="si_max" value="21" /> 194 <conditional name="source">
200 <param name="pi_min" value="23" /> 195 <param name="source" value="history" />
201 <param name="pi_max" value="29" /> 196 <param name="file" value ="genome-small.fa" />
202 <param name="mis" value="0" /> 197 </conditional>
203 <param name="misTE" value="3" /> 198 <param name="mis" value="0" />
199 </section>
200 <section name="transcripts">
201 <conditional name="source">
202 <param name="source" value="history" />
203 <param name="file" value ="transcripts-file-small.fa" />
204 </conditional>
205 </section>
206 <section name="te">
207 <conditional name="source">
208 <param name="source" value="history" />
209 <param name="file" value ="TE-file-small.fa" />
210 </conditional>
211 <param name="misTE" value="3" />
212 </section>
213 <section name="mirnas">
214 <conditional name="source">
215 <param name="source" value="history" />
216 <param name="file" value ="mirbase-21-dme-hairpins-16jul2015.fa" />
217 </conditional>
218 </section>
219 <section name="snrnas">
220 <conditional name="snrnas">
221 <param name="use_ref" value="true"/>
222 <conditional name="source">
223 <param name="source" value="history" />
224 <param name="file" value ="dmel-all-sn-snoRNA-r6.03.fasta" />
225 </conditional>
226 </conditional>
227 </section>
228 <section name="rrnas">
229 <conditional name="rrnas">
230 <param name="use_ref" value="true"/>
231 <conditional name="source">
232 <param name="source" value="history" />
233 <param name="file" value ="dmel-all-rRNA-r6.03.fasta" />
234 </conditional>
235 </conditional>
236 </section>
237 <section name="trnas">
238 <conditional name="trnas">
239 <param name="use_ref" value="true"/>
240 <conditional name="source">
241 <param name="source" value="history" />
242 <param name="file" value ="dmel-all-tRNA-r6.03.fasta" />
243 </conditional>
244 </conditional>
245 </section>
246 <section name="sirna">
247 <param name="si_min" value="21" />
248 <param name="si_max" value="21" />
249 </section>
250 <section name="pirna">
251 <param name="pi_min" value="23" />
252 <param name="pi_max" value="29" />
253 </section>
204 <param name="PPPon" value="true" /> 254 <param name="PPPon" value="true" />
205 <output name='html_out' file="res.html" compare='diff' lines_diff = '10'/> 255 <output name='html_out' file="res.html" compare='diff' lines_diff = '10'/>
206 <output_collection name="output_fastqsanger" type="list"> 256 <output_collection name="output_fastqsanger" type="list">
207 <element name="reads-sample-small.fastq_all_mappers" file="fastq_dir/reads-sample-small.fastq_all_mappers.fastq" /> 257 <element name="reads-sample-small.fastq_all_mappers" file="fastq_dir/reads-sample-small.fastq_all_mappers.fastq" />
208 <element name="reads-sample-small.fastq-bonafide_reads-genome" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-genome.fastq" /> 258 <element name="reads-sample-small.fastq-bonafide_reads-genome" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-genome.fastq" />