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comparison locarna_reliability_profile.xml @ 4:7d63908343c3 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 94c141a71ef115279f1090f782b6f5cdeea9c277
author bgruening
date Mon, 19 Aug 2024 18:52:31 +0000
parents e84d1fc87829
children
comparison
equal deleted inserted replaced
3:e84d1fc87829 4:7d63908343c3
4 </description> 4 </description>
5 5
6 <macros> 6 <macros>
7 <import>macros.xml</import> 7 <import>macros.xml</import>
8 </macros> 8 </macros>
9
10 <expand macro="requirements" /> 9 <expand macro="requirements" />
11
12 <expand macro="stdio" /> 10 <expand macro="stdio" />
13
14 <expand macro="version" /> 11 <expand macro="version" />
15 12
16 <command><![CDATA[ 13 <command><![CDATA[
17 (if file '$input_archive' | grep 'gzip compressed' > /dev/null ; 14 (if file '$input_archive' | grep 'gzip compressed' > /dev/null ;
18 then tar xzf '$input_archive' ; 15 then tar xzf '$input_archive' ;
61 58
62 > '$stdout' 59 > '$stdout'
63 ]]></command> 60 ]]></command>
64 61
65 <inputs> 62 <inputs>
66 <param name="input_archive" type="data" format="tar.gz" label="MLocARNA archive" 63 <param name="input_archive" type="data" format="tar.gz" label="MLocARNA archive" help="Archive of MLocARNA results (tar or tar.gz as generated by running mlocarna in probabilistic alignment mode)."/>
67 help="Archive of MLocARNA results (tar or tar.gz as generated by running 64 <param name="title" type="text" label="Plot title" help="Title of the plot"/>
68 mlocarna in probabilistic alignment mode)." /> 65 <param name="seqname" type="text" label="Reference sequence" help="Project to a reference sequence. Provide one of the sequence names in the alignment input or leave blank to plot without projection."/>
69 66 <param argument="--dont-predict" name="predict" type="boolean" checked="true" truevalue="" falsevalue="--dont-predict" help="Turn on/off predicting."/>
70 <param name="title" type="text" label="Plot title" 67 <param argument="--fit-once-on" type="boolean" checked="false" truevalue="--fit-once-on" falsevalue="" help="Predict exactly one 'on'-region"/>
71 help="Title of the plot" 68 <param argument="--show-sw" type="boolean" checked="true" truevalue="--show-sw" falsevalue="" help="Show the influence of structure weight."/>
72 /> 69 <param argument="--revcompl" name="rev_compl" type="boolean" checked="false" truevalue="--revcompl" falsevalue="" help="Plot and fit a reverse complement."/>
73 70 <param argument="--beta" help="Inverse temperature for fitting." type="float" value="12.0" min="1.0" max="25.0"/>
74 <param name="seqname" type="text" label="Reference sequence" 71 <param argument="--structure-weight" type="float" value="1.0" min="0.0" max="8.0" help="Weight of structure against sequence (1.0 means equal)"/>
75 help="Project to a reference sequence. Provide one of the sequence names in the alignment input 72 <param argument="--offset" help="Genomic offset." type="integer" value="1"/>
76 or leave blank to plot without projection." 73 <param argument="--signals" type="text" label="List of signals" help="List of '{from to} orientation' signal specifications. Show signals in plot and compared infered signal to them. Ranges 'from to' can be repeated; the orientation must be either +1 or -1.The specifications of the single signals are separated by ';'. Example of two signal,where the first one consists of two ranges: 1 15 20 30 +1; 15 45 -1">
77 />
78
79 <param argument="--dont-predict" name="predict" type="boolean" checked="true"
80 truevalue="" falsevalue="--dont-predict"
81 help="Turn on/off predicting."
82 />
83
84 <param argument="--fit-once-on" type="boolean" checked="false"
85 truevalue="--fit-once-on" falsevalue=""
86 help="Predict exactly one 'on'-region"
87 />
88
89 <param argument="--show-sw" type="boolean" checked="true"
90 truevalue="--show-sw" falsevalue=""
91 help="Show the influence of structure weight."
92 />
93
94 <param argument="--revcompl" name="rev_compl" type="boolean" checked="false"
95 truevalue="--revcompl" falsevalue=""
96 help="Plot and fit a reverse complement."
97 />
98
99 <param argument="--beta" help="Inverse temperature for fitting."
100 type="float" value="12.0" min="1.0" max="25.0" />
101
102 <param argument="--structure-weight"
103 type="float" value="1.0" min="0.0" max="8.0"
104 help="Weight of structure against sequence (1.0 means equal)"
105 />
106
107 <param argument="--offset" help="Genomic offset."
108 type="integer" value="1" />
109
110 <param argument="--signals" type="text" label="List of signals"
111 help="List of '{from to} orientation' signal specifications. Show signals in plot
112 and compared infered signal to them. Ranges 'from to' can be repeated;
113 the orientation must be either +1 or -1.
114 The specifications of the single signals are separated by ';'. Example of two signal,
115 where the first one consists of two ranges: 1 15 20 30 +1; 15 45 -1"
116 >
117 <sanitizer invalid_char=" "> 74 <sanitizer invalid_char=" ">
118 <valid initial="string.digits"> <add value="+" /> <add value="-" /> <add value=";" /> </valid> 75 <valid initial="string.digits"> <add value="+" /> <add value="-" /> <add value=";" /> </valid>
119 </sanitizer> 76 </sanitizer>
120 </param> 77 </param>
121 78
122 <param name="output_format" type="select" 79 <param name="output_format" type="select" label="Output options">
123 label="Output options"> 80 <option value="pdf" selected="true">Plot in pdf format</option>
124 <option value="pdf" selected="true">Plot in pdf
125 format</option>
126 <option value="png" selected="false">Plot in png format</option> 81 <option value="png" selected="false">Plot in png format</option>
127 </param> 82 </param>
128 83
129 <param name="write_rscript" type="boolean" argument="--write-R-script" 84 <param name="write_rscript" type="boolean" argument="--write-R-script" label="Write R script" checked="false" help="Write R script that can produce the output plot."/>
130 label="Write R script" checked="false" 85 <param name="write_subsequence" type="boolean" argument="--write-subseq" label="Write Subsequence" checked="false" help="Write subsequence in output."/>
131 help="Write R script that can produce the output plot."
132 />
133
134 <param name="write_subsequence" type="boolean" argument="--write-subseq"
135 label="Write Subsequence" checked="false"
136 help="Write subsequence in output."
137 />
138
139 </inputs> 86 </inputs>
140 87
141 88
142 <outputs> 89 <outputs>
143 <data format="pdf" name="pdf_output_plot" 90 <data format="pdf" name="pdf_output_plot" label="${tool.name} on ${on_string}: PDF plot">
144 label="${tool.name} on ${on_string}: plot">
145 <filter>output_format == 'pdf'</filter> 91 <filter>output_format == 'pdf'</filter>
146 </data> 92 </data>
147 <data format="png" name="png_output_plot" 93 <data format="png" name="png_output_plot" label="${tool.name} on ${on_string}: PNG plot">
148 label="${tool.name} on ${on_string}: plot">
149 <filter>output_format == 'png'</filter> 94 <filter>output_format == 'png'</filter>
150 </data> 95 </data>
151 <data format="txt" name="rscript_output" 96 <data format="txt" name="rscript_output" label="${tool.name} on ${on_string}: R script ">
152 label="${tool.name} on ${on_string}: R script ">
153 <filter> write_rscript is True </filter> 97 <filter> write_rscript is True </filter>
154 </data> 98 </data>
155 <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout" /> 99 <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout" />
156 </outputs> 100 </outputs>
157 101