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comparison Marea/marea.xml @ 28:e6831924df01 draft

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small fixes (elbow plot and output managment)
author bimib
date Mon, 14 Oct 2019 05:01:08 -0400
parents 100c116d0d25
children 9fcb0e8d6d47
comparison
equal deleted inserted replaced
27:8c480c977a12 28:e6831924df01
52 #end for 52 #end for
53 #elif $cond.type_selector == 'dataset_class': 53 #elif $cond.type_selector == 'dataset_class':
54 --input_data ${input_data} 54 --input_data ${input_data}
55 --input_class ${input_class} 55 --input_class ${input_class}
56 #end if 56 #end if
57 #if $cond.type_selector == 'datasets_rasonly':
58 --input_datas ${input_Datasets}
59 --single_ras_file $ras_single
60 #end if
57 ]]> 61 ]]>
58 </command> 62 </command>
59 63
60 <inputs> 64 <inputs>
61 <conditional name="cond_rule"> 65 <conditional name="cond_rule">
81 </conditional> 85 </conditional>
82 <conditional name="cond"> 86 <conditional name="cond">
83 <param name="type_selector" argument="--option" type="select" label="Input format:"> 87 <param name="type_selector" argument="--option" type="select" label="Input format:">
84 <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N</option> 88 <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N</option>
85 <option value="dataset_class">RNAseq of all samples + sample group specification</option> 89 <option value="dataset_class">RNAseq of all samples + sample group specification</option>
90 <option value="datasets_rasonly" selected="true">RNAseq dataset</option>
86 </param> 91 </param>
87 <when value="datasets"> 92 <when value="datasets">
88 <repeat name="input_Datasets" title="RNAseq" min="2"> 93 <repeat name="input_Datasets" title="RNAseq" min="2">
89 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" /> 94 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
90 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" /> 95 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
91 </repeat> 96 </repeat>
92 </when> 97 </when>
98 <when value="datasets_rasonly">
99 <param name="input_Datasets" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
100 </when>
93 <when value="dataset_class"> 101 <when value="dataset_class">
94 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" /> 102 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
95 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" /> 103 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
96 </when> 104 </when>
97 </conditional> 105 </conditional>
106
107
108 <!--TODO: NASCONDERE ADVANCED SE RAS ONLY-->
98 109
99 <conditional name="advanced"> 110 <conditional name="advanced">
100 <param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom rules for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps."> 111 <param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom rules for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps.">
101 <option value="true" selected="true">No</option> 112 <option value="true" selected="true">No</option>
102 <option value="false">Yes</option> 113 <option value="false">Yes</option>
114 </conditional> 125 </conditional>
115 </inputs> 126 </inputs>
116 127
117 <outputs> 128 <outputs>
118 <data format="txt" name="log" label="${tool.name} - Log" /> 129 <data format="txt" name="log" label="${tool.name} - Log" />
130 <data format="tabular" name="ras_single" label="${tool.name} - RAS">
131 <filter>cond['type_selector'] == "datasets_rasonly"</filter>
132 </data>
119 <collection name="results" type="list" label="${tool.name} - Results"> 133 <collection name="results" type="list" label="${tool.name} - Results">
134 <filter>cond['type_selector'] == "datasets" or cond['type_selector'] == "dataset_class"</filter>
120 <discover_datasets pattern="__name_and_ext__" directory="result"/> 135 <discover_datasets pattern="__name_and_ext__" directory="result"/>
121 </collection> 136 </collection>
122 <collection name="ras" type="list" label="${tool.name} - RAS" format_source="tabular"> 137 <collection name="ras" type="list" label="${tool.name} - RAS list" format_source="tabular">
123 <filter>advanced['choice'] and advanced['generateRas']</filter> 138 <filter>advanced['choice'] and advanced['generateRas']</filter>
124 <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/> 139 <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/>
125 </collection> 140 </collection>
141
126 </outputs> 142 </outputs>
127 <tests> 143 <tests>
128 <test> 144 <test>
129 <param name="pValue" value="0.56"/> 145 <param name="pValue" value="0.56"/>
130 <output name="log" file="log.txt"/> 146 <output name="log" file="log.txt"/>