Mercurial > repos > brasset_jensen > srnapipe

comparison sRNAPipe.xml @ 14:cc66a625989f draft

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Uploaded
author brasset_jensen
date Fri, 26 Jan 2018 08:08:24 -0500
parents cbd6577652a5
children 9f6ece278d09
comparison
equal deleted inserted replaced
13:a4a170bc040f 14:cc66a625989f
19 #end if 19 #end if
20 20
21 #if $tRNAs.refGenomeSource == "history": 21 #if $tRNAs.refGenomeSource == "history":
22 --tRNAs "${tRNAs.ownFile}" 22 --tRNAs "${tRNAs.ownFile}"
23 --build_tRNAs 23 --build_tRNAs
24 #elif $tRNAs.refGenomeSource == "none":
25 --tRNAs "None"
24 #else: 26 #else:
25 --tRNAs "${tRNAs.indices.fields.path}" 27 --tRNAs "${tRNAs.indices.fields.path}"
26 #end if 28 #end if
27 29
28 #if $snRNAs.refGenomeSource == "history": 30 #if $snRNAs.refGenomeSource == "history":
29 --snRNAs "${snRNAs.ownFile}" 31 --snRNAs "${snRNAs.ownFile}"
30 --build_snRNAs 32 --build_snRNAs
33 #elif $snRNAs.refGenomeSource == "none":
34 --snRNAs "None"
31 #else: 35 #else:
32 --snRNAs "${snRNAs.indices.fields.path}" 36 --snRNAs "${snRNAs.indices.fields.path}"
37 #end if
38
39 #if $rRNAs.refGenomeSource == "history":
40 --rRNAs "${rRNAs.ownFile}"
41 --build_rRNAs
42 #elif $rRNAs.refGenomeSource == "none":
43 --rRNAs "None"
44 #else:
45 --rRNAs "${rRNAs.indices.fields.path}"
33 #end if 46 #end if
34 47
35 #if $miRNAs.refGenomeSource == "history": 48 #if $miRNAs.refGenomeSource == "history":
36 --miRNAs "${miRNAs.ownFile}" 49 --miRNAs "${miRNAs.ownFile}"
37 --build_miRNAs 50 --build_miRNAs
49 #if $TE.refGenomeSource == "history": 62 #if $TE.refGenomeSource == "history":
50 --TE "${TE.ownFile}" 63 --TE "${TE.ownFile}"
51 --build_TE 64 --build_TE
52 #else: 65 #else:
53 --TE "${TE.indices.fields.path}" 66 --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 67 #end if
62 68
63 --si_min $si_min 69 --si_min $si_min
64 --si_max $si_max 70 --si_max $si_max
65 --pi_min $pi_min 71 --pi_min $pi_min
100 </when> 106 </when>
101 <when value="history"> 107 <when value="history">
102 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> 108 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
103 </when> 109 </when>
104 </conditional> 110 </conditional>
111 <conditional name="transcripts">
112 <param name="refGenomeSource" type="select" label="Will you select transcripts database from your history or use a built-in index?">
113 <option value="indexed">Use a built-in index</option>
114 <option value="history">Use one from the history</option>
115 </param>
116 <when value="indexed">
117 <param name="indices" type="select" label="Select a transcripts reference">
118 <options from_data_table="bwa_indexes">
119 <filter type="sort_by" column="2" />
120 <validator type="no_options" message="No indexes are available" />
121 </options>
122 </param>
123 </when>
124 <when value="history">
125 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
126 </when>
127 </conditional>
105 <conditional name="TE"> 128 <conditional name="TE">
106 <param name="refGenomeSource" type="select" label="Will you select TE database from your history or use a built-in index?"> 129 <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> 130 <option value="indexed">Use a built-in index</option>
108 <option value="history">Use one from the history</option> 131 <option value="history">Use one from the history</option>
109 </param> 132 </param>
138 </conditional> 161 </conditional>
139 <conditional name="snRNAs"> 162 <conditional name="snRNAs">
140 <param name="refGenomeSource" type="select" label="Will you select snRNA database from your history or use a built-in index?"> 163 <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> 164 <option value="indexed">Use a built-in index</option>
142 <option value="history">Use one from the history</option> 165 <option value="history">Use one from the history</option>
166 <option value="none">None</option>
143 </param> 167 </param>
144 <when value="indexed"> 168 <when value="indexed">
145 <param name="indices" type="select" label="Select a snRNAs reference"> 169 <param name="indices" type="select" label="Select a snRNAs reference">
146 <options from_data_table="bwa_indexes"> 170 <options from_data_table="bwa_indexes">
147 <filter type="sort_by" column="2" /> 171 <filter type="sort_by" column="2" />
155 </conditional> 179 </conditional>
156 <conditional name="rRNAs"> 180 <conditional name="rRNAs">
157 <param name="refGenomeSource" type="select" label="Will you select rRNAs database from your history or use a built-in index?"> 181 <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> 182 <option value="indexed">Use a built-in index</option>
159 <option value="history">Use one from the history</option> 183 <option value="history">Use one from the history</option>
184 <option value="none">None</option>
160 </param> 185 </param>
161 <when value="indexed"> 186 <when value="indexed">
162 <param name="indices" type="select" label="Select a rRNAs reference"> 187 <param name="indices" type="select" label="Select a rRNAs reference">
163 <options from_data_table="bwa_indexes"> 188 <options from_data_table="bwa_indexes">
164 <filter type="sort_by" column="2" /> 189 <filter type="sort_by" column="2" />
172 </conditional> 197 </conditional>
173 <conditional name="tRNAs"> 198 <conditional name="tRNAs">
174 <param name="refGenomeSource" type="select" label="Will you select tRNA database from your history or use a built-in index?"> 199 <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> 200 <option value="indexed">Use a built-in index</option>
176 <option value="history">Use one from the history</option> 201 <option value="history">Use one from the history</option>
202 <option value="none">None</option>
177 </param> 203 </param>
178 <when value="indexed"> 204 <when value="indexed">
179 <param name="indices" type="select" label="Select a tRNA reference"> 205 <param name="indices" type="select" label="Select a tRNA reference">
180 <options from_data_table="bwa_indexes"> 206 <options from_data_table="bwa_indexes">
181 <filter type="sort_by" column="2" /> 207 <filter type="sort_by" column="2" />
185 </when> 211 </when>
186 <when value="history"> 212 <when value="history">
187 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> 213 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
188 </when> 214 </when>
189 </conditional> 215 </conditional>
190 <conditional name="transcripts"> 216
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"/> 217 <param name="min" type="integer" value="18" label="minimum read size"/>
208 <param name="max" type="integer" value="29" label="maximum read size"/> 218 <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"/> 219 <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"/> 220 <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"/> 221 <param name="pi_min" type="integer" value="23" label="lower bound of piRNA range"/>