Mercurial > repos > brasset_jensen > srnapipe

comparison sRNAPipe.xml @ 70:be25d16676f6 draft

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"planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 1b35c33c35e4d5e11764941c277edd2e1f97f729"
author brasset_jensen
date Thu, 06 Feb 2020 10:32:47 -0500
parents fa794d2a5aaf
children 71d5983dd41e
comparison
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69:fa794d2a5aaf 70:be25d16676f6
32 <when value="false"/> 32 <when value="false"/>
33 </conditional> 33 </conditional>
34 </xml> 34 </xml>
35 </macros> 35 </macros>
36 <requirements> 36 <requirements>
37 <requirement type="package" version="1.1">srnapipe</requirement> 37 <requirement type="package" version="1.1.1">srnapipe</requirement>
38 </requirements> 38 </requirements>
39 <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>
40 <command detect_errors="aggressive"><![CDATA[ 40 <command detect_errors="aggressive"><![CDATA[
41 srnapipe 41 srnapipe
42 #if str($inputs.custom) == 'true' 42 #if str($inputs.custom) == 'true'
88 --snRNAs '$snrnas.snrnas.source.file' 88 --snRNAs '$snrnas.snrnas.source.file'
89 --build_snRNAs 89 --build_snRNAs
90 #else 90 #else
91 --snRNAs '$snrnas.snrnas.source.indices.fields.path' 91 --snRNAs '$snrnas.snrnas.source.indices.fields.path'
92 #end if 92 #end if
93 #else
94 --snRNAs "None"
95 #end if 93 #end if
96 94
97 #if str($rrnas.rrnas.use_ref) == 'true' 95 #if str($rrnas.rrnas.use_ref) == 'true'
98 #if str($rrnas.rrnas.source.source) == "history" 96 #if str($rrnas.rrnas.source.source) == "history"
99 --rRNAs '$rrnas.rrnas.source.file' 97 --rRNAs '$rrnas.rrnas.source.file'
100 --build_rRNAs 98 --build_rRNAs
101 #else 99 #else
102 --rRNAs '$rrnas.rrnas.source.indices.fields.path' 100 --rRNAs '$rrnas.rrnas.source.indices.fields.path'
103 #end if 101 #end if
104 #else
105 --rRNAs "None"
106 #end if 102 #end if
107 103
108 #if str($trnas.trnas.use_ref) == 'true' 104 #if str($trnas.trnas.use_ref) == 'true'
109 #if str($trnas.trnas.source.source) == "history" 105 #if str($trnas.trnas.source.source) == "history"
110 --tRNAs '$trnas.trnas.source.file' 106 --tRNAs '$trnas.trnas.source.file'
111 --build_tRNAs 107 --build_tRNAs
112 #else 108 #else
113 --tRNAs '$trnas.trnas.source.indices.fields.path' 109 --tRNAs '$trnas.trnas.source.indices.fields.path'
114 #end if 110 #end if
115 #else
116 --tRNAs "None"
117 #end if 111 #end if
118 112
119 --si_min $sirna.si_min 113 --si_min $sirna.si_min
120 --si_max $sirna.si_max 114 --si_max $sirna.si_max
121 --pi_min $pirna.pi_min 115 --pi_min $pirna.pi_min
122 --pi_max $pirna.pi_max 116 --pi_max $pirna.pi_max
123 --dir $html_out.files_path 117 --dir $html_out.files_path
124 --html $html_out 118 --html $html_out
125 --PPPon $PPPon 119 --PPPon $PPPon
120 --threads '\${GALAXY_SLOTS:-4}'
126 ]]> 121 ]]>
127 </command> 122 </command>
128 <inputs> 123 <inputs>
129 <conditional name="inputs"> 124 <conditional name="inputs">
130 <param name="custom" type="select" label="Use custom name for the input sequence files?"> 125 <param name="custom" type="select" label="Use custom name for the input sequence files?">