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comparison cummerbund_wrapper.xml @ 2:5de9fff7ccf7

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fix for warnings on empty conditional inputs
author Carlos Borroto <carlos.borroto@gmail.com>
date Tue, 14 Feb 2012 13:00:16 -0500
parents 6e2abd76a853
children f4e2d805434c
comparison
equal deleted inserted replaced
1:65940895e1c6 2:5de9fff7ccf7
1 <tool id="cummerbund" name="cummeRbund" version="0.0.1"> 1 <tool id="cummerbund" name="cummeRbund" version="0.0.2">
2 <description>is an R package that is designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output</description> 2
3 <description>R package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output</description>
4
3 <command interpreter="python"> 5 <command interpreter="python">
4 cummerbund_wrapper.py 6 cummerbund_wrapper.py
5 --r-script ${script_file} 7 --r-script ${script_file}
6 --html-report-from-directory "${output_html}" "${output_html.files_path}" 8 --html-report-from-directory "${output_html}" "${output_html.files_path}"
7 </command> 9 </command>
10
8 <inputs> 11 <inputs>
9 <conditional name="backend_database_source"> 12 <conditional name="backend_database_source">
10 <param name="backend_database_selector" type="select" label="Will you select a backend database file from the history or do you want to build a new one using cuffdiff output?"> 13 <param name="backend_database_selector" type="select" label="Will you select a backend database file from the history or do you want to build a new one using cuffdiff output?">
11 <option value="history" selected="true">Use backend database from the history</option> 14 <option value="history" selected="true">Use backend database from the history</option>
12 <option value="cuffdiff_output">Build backend database using cuffdiff output</option> 15 <option value="cuffdiff_output">Build backend database using cuffdiff output</option>
42 <option value="cluster">Cluster</option> 45 <option value="cluster">Cluster</option>
43 <option value="expressionplot">Expression Plot</option> 46 <option value="expressionplot">Expression Plot</option>
44 <option value="expressionbarplot">Expression Bar Plot</option> 47 <option value="expressionbarplot">Expression Bar Plot</option>
45 </param> 48 </param>
46 <when value="density"> 49 <when value="density">
50 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
47 </when> 51 </when>
48 <when value="boxplot"> 52 <when value="boxplot">
53 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
49 </when> 54 </when>
50 <when value="scatter"> 55 <when value="scatter">
51 <param name="x" type="text" label="Sample name for x axis"/> 56 <param name="x" type="text" label="Sample name for x axis"/>
52 <param name="y" type="text" label="Sample name for y axis"/> 57 <param name="y" type="text" label="Sample name for y axis"/>
58 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
53 <param name="smooth" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Add a smooth-fit regression line"/> 59 <param name="smooth" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Add a smooth-fit regression line"/>
54 <conditional name="multiple_genes"> 60 <conditional name="multiple_genes">
55 <param name="multiple_genes_selector" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Limit plot to a group of genes?"/> 61 <param name="multiple_genes_selector" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Limit plot to a group of genes?"/>
56 <when value="T"> 62 <when value="T">
57 <param name="features" type="select" label="Expression levels to plot?"> 63 <param name="features" type="select" label="Expression levels to plot?">
89 <option value="gene" selected="true">Genes</option> 95 <option value="gene" selected="true">Genes</option>
90 <option value="isoforms">Isoforms</option> 96 <option value="isoforms">Isoforms</option>
91 <option value="tss">TSS</option> 97 <option value="tss">TSS</option>
92 <option value="cds">CDS</option> 98 <option value="cds">CDS</option>
93 </param> 99 </param>
100 <repeat name="genes" title="Genes">
101 <param name="gene_id" type="text" label="Gene ID"/>
102 </repeat>
94 <param name="clustering" type="select" label="Cluster by"> 103 <param name="clustering" type="select" label="Cluster by">
95 <option value="row">Row</option> 104 <option value="row">Row</option>
96 <option value="column">Column</option> 105 <option value="column">Column</option>
97 <option value="both" selected="true">Both</option> 106 <option value="both" selected="true">Both</option>
98 <option value="none">None</option> 107 <option value="none">None</option>
99 </param> 108 </param>
100 <param name="labcol" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/> 109 <param name="labcol" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/>
101 <param name="labrow" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/> 110 <param name="labrow" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/>
111 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
102 <param name="border" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw border around plot?"/> 112 <param name="border" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw border around plot?"/>
113 </when>
114 <when value="cluster">
115 <param name="features" type="select" label="Expression levels to plot?">
116 <option value="gene" selected="true">Genes</option>
117 <option value="isoforms">Isoforms</option>
118 <option value="tss">TSS</option>
119 <option value="cds">CDS</option>
120 </param>
103 <repeat name="genes" title="Genes"> 121 <repeat name="genes" title="Genes">
104 <param name="gene_id" type="text" label="Gene ID"/> 122 <param name="gene_id" type="text" label="Gene ID"/>
105 </repeat> 123 </repeat>
106 </when>
107 <when value="cluster">
108 <param name="features" type="select" label="Expression levels to plot?">
109 <option value="gene" selected="true">Genes</option>
110 <option value="isoforms">Isoforms</option>
111 <option value="tss">TSS</option>
112 <option value="cds">CDS</option>
113 </param>
114 <param name="k" type="text" label="Number of pre-defined clusters to attempt to find."/> 124 <param name="k" type="text" label="Number of pre-defined clusters to attempt to find."/>
115 <param name="iter_max" type="text" value="100" label="Max iterations"/> 125 <param name="iter_max" type="text" value="100" label="Max iterations"/>
116 <repeat name="genes" title="Genes">
117 <param name="gene_id" type="text" label="Gene ID"/>
118 </repeat>
119 </when> 126 </when>
120 <when value="expressionplot"> 127 <when value="expressionplot">
121 <param name="features" type="select" label="Expression levels to plot?"> 128 <param name="features" type="select" label="Expression levels to plot?">
122 <option value="gene" selected="true">Genes</option> 129 <option value="gene" selected="true">Genes</option>
123 <option value="isoforms">Isoforms</option> 130 <option value="isoforms">Isoforms</option>
124 <option value="tss">TSS</option> 131 <option value="tss">TSS</option>
125 <option value="cds">CDS</option> 132 <option value="cds">CDS</option>
126 </param> 133 </param>
134 <param name="gene_id" type="text" label="Gene ID"/>
135 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
127 <param name="draw_summary" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw a 'summary' line with mean FPKM 136 <param name="draw_summary" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw a 'summary' line with mean FPKM
128 values for each condition?"/> 137 values for each condition?"/>
129 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/> 138 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/>
139 </when>
140 <when value="expressionbarplot">
141 <param name="features" type="select" label="Expression levels to plot?">
142 <option value="gene" selected="true">Genes</option>
143 <option value="isoforms">Isoforms</option>
144 <option value="tss">TSS</option>
145 <option value="cds">CDS</option>
146 </param>
130 <param name="gene_id" type="text" label="Gene ID"/> 147 <param name="gene_id" type="text" label="Gene ID"/>
131 </when> 148 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
132 <when value="expressionbarplot">
133 <param name="features" type="select" label="Expression levels to plot?">
134 <option value="gene" selected="true">Genes</option>
135 <option value="isoforms">Isoforms</option>
136 <option value="tss">TSS</option>
137 <option value="cds">CDS</option>
138 </param>
139 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/> 149 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/>
140 <param name="gene_id" type="text" label="Gene ID"/>
141 </when> 150 </when>
142 </conditional> 151 </conditional>
143 </repeat> 152 </repeat>
144 </inputs> 153 </inputs>
154
145 <outputs> 155 <outputs>
146 <data format="data" name="output_database" label="${tool.name} on ${on_string}: Database File (sqlite)"> 156 <data format="data" name="output_database" label="${tool.name} on ${on_string}: Database File (sqlite)">
147 <filter>backend_database_source['backend_database_selector'] == "cuffdiff_output"</filter> 157 <filter>backend_database_source['backend_database_selector'] == "cuffdiff_output"</filter>
148 </data> 158 </data>
149 <data format="html" name="output_html" label="${tool.name} on ${on_string} (HTML)"/> 159 <data format="html" name="output_html" label="${tool.name} on ${on_string} (HTML)"/>