Mercurial > repos > yhoogstrate > edger_with_design_matrix

comparison edgeR_Differential_Gene_Expression.xml @ 72:e75afef75c13 draft

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author yhoogstrate
date Tue, 30 Sep 2014 11:24:28 -0400
parents fb64bf85361d
children 83e20cbce42a
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71:46896caca6be 72:e75afef75c13
5 <requirements> 5 <requirements>
6 <!--<requirement type="package" version="3.0.1">package_r3_withx</requirement>--> 6 <!--<requirement type="package" version="3.0.1">package_r3_withx</requirement>-->
7 <!--<requirement type="package" version="3.1.0">R</requirement>--> 7 <!--<requirement type="package" version="3.1.0">R</requirement>-->
8 <requirement type="package" version="3.0.3">R</requirement> 8 <requirement type="package" version="3.0.3">R</requirement>
9 <requirement type="package" version="latest">package_biocLite_edgeR_limma</requirement> 9 <requirement type="package" version="latest">package_biocLite_edgeR_limma</requirement>
10 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
11 </package>
12 -->
10 </requirements> 13 </requirements>
11 14
12 <command> 15 <command>
13 <!-- 16 <!--
14 The following script is written in the "Cheetah" language: 17 The following script is written in the "Cheetah" language:
89 echo "Converting PDF figures to PNG" ; 92 echo "Converting PDF figures to PNG" ;
90 93
91 #if $output_MDSplot: 94 #if $output_MDSplot:
92 #set $output_MDSplot_tmp = str($output_MDSplot)+".png" 95 #set $output_MDSplot_tmp = str($output_MDSplot)+".png"
93 96
94 convert $output_MDSplot $output_MDSplot_tmp ; 97 gm convert $output_MDSplot $output_MDSplot_tmp ;
95 mv $output_MDSplot_tmp $output_MDSplot ; 98 mv $output_MDSplot_tmp $output_MDSplot ;
96 #end if 99 #end if
97 100
98 #if $output_BCVplot: 101 #if $output_BCVplot:
99 #set $output_BCVplot_tmp = str($output_BCVplot)+".png" 102 #set $output_BCVplot_tmp = str($output_BCVplot)+".png"
100 103
101 convert $output_BCVplot $output_BCVplot_tmp ; 104 gm convert $output_BCVplot $output_BCVplot_tmp ;
102 mv $output_BCVplot_tmp $output_BCVplot ; 105 mv $output_BCVplot_tmp $output_BCVplot ;
103 #end if 106 #end if
104 107
105 #if $output_MAplot: 108 #if $output_MAplot:
106 #set $output_MAplot_tmp = str($output_MAplot)+".png" 109 #set $output_MAplot_tmp = str($output_MAplot)+".png"
107 110
108 convert $output_MAplot $output_MAplot_tmp ; 111 gm convert $output_MAplot $output_MAplot_tmp ;
109 mv $output_MAplot_tmp $output_MAplot ; 112 mv $output_MAplot_tmp $output_MAplot ;
110 #end if 113 #end if
111 114
112 #if $output_PValue_distribution_plot: 115 #if $output_PValue_distribution_plot:
113 #set $output_PValue_distribution_plot_tmp = str($output_PValue_distribution_plot)+".png" 116 #set $output_PValue_distribution_plot_tmp = str($output_PValue_distribution_plot)+".png"
114 117
115 convert $output_PValue_distribution_plot $output_PValue_distribution_plot_tmp ; 118 gm convert $output_PValue_distribution_plot $output_PValue_distribution_plot_tmp ;
116 mv $output_PValue_distribution_plot_tmp $output_PValue_distribution_plot ; 119 mv $output_PValue_distribution_plot_tmp $output_PValue_distribution_plot ;
117 #end if 120 #end if
118 121
119 #if $output_hierarchical_clustering_plot: 122 #if $output_hierarchical_clustering_plot:
120 #set $output_hierarchical_clustering_plot_tmp = str($output_hierarchical_clustering_plot)+".png" 123 #set $output_hierarchical_clustering_plot_tmp = str($output_hierarchical_clustering_plot)+".png"
121 124
122 convert $output_hierarchical_clustering_plot $output_hierarchical_clustering_plot_tmp ; 125 gm convert $output_hierarchical_clustering_plot $output_hierarchical_clustering_plot_tmp ;
123 mv $output_hierarchical_clustering_plot_tmp $output_hierarchical_clustering_plot ; 126 mv $output_hierarchical_clustering_plot_tmp $output_hierarchical_clustering_plot ;
124 #end if 127 #end if
125 128
126 #if $output_heatmap_plot: 129 #if $output_heatmap_plot:
127 #set $output_heatmap_plot_tmp = str($output_heatmap_plot)+".png" 130 #set $output_heatmap_plot_tmp = str($output_heatmap_plot)+".png"
128 131
129 convert $output_heatmap_plot $output_heatmap_plot_tmp ; 132 gm convert $output_heatmap_plot $output_heatmap_plot_tmp ;
130 mv $output_heatmap_plot_tmp $output_heatmap_plot ; 133 mv $output_heatmap_plot_tmp $output_heatmap_plot ;
131 #end if 134 #end if
132 #end if 135 #end if
133 136
134 grep -v 'Calculating library sizes from column' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 137 grep -v 'Calculating library sizes from column' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ;
141 grep -v 'Setting LC_MEASUREMENT failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 144 grep -v 'Setting LC_MEASUREMENT failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ;
142 grep -v 'Setting LC_CTYPE failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 145 grep -v 'Setting LC_CTYPE failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ;
143 grep -v 'Setting LC_COLLATE failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 146 grep -v 'Setting LC_COLLATE failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ;
144 147
145 cat stderr.txt >&amp;2 148 cat stderr.txt >&amp;2
146 149
147 </command> 150 </command>
148 151
149 <inputs> 152 <inputs>
150 <param name="expression_matrix" type="data" format="tabular" label="Expression (read count) matrix" /> 153 <param name="expression_matrix" type="data" format="tabular" label="Expression (read count) matrix" />
151 <param name="design_matrix" type="data" format="tabular" label="Design matrix" hepl="Ensure your samplenames are identical to those in the expression matrix. Preferentially, create the contrast matrix using 'edgeR: Design- from Expression matrix'." /> 154 <param name="design_matrix" type="data" format="tabular" label="Design matrix" hepl="Ensure your samplenames are identical to those in the expression matrix. Preferentially, create the contrast matrix using 'edgeR: Design- from Expression matrix'." />