Mercurial > repos > yhoogstrate > edger_with_design_matrix

comparison edgeR_Differential_Gene_Expression.xml @ 90:f87938c392bf draft

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Hardcoded the png: suffix for gm convert, to ensure conversion to png
author yhoogstrate
date Wed, 28 Jan 2015 09:43:55 -0500
parents 875f080136b6
children c81da57fff20
comparison
equal deleted inserted replaced
89:875f080136b6 90:f87938c392bf
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.0.3-latest.b"> 2 <tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.0.3-latest.c">
3 <description>RNA-Seq gene expression analysis using edgeR (R package)</description> 3 <description>RNA-Seq gene expression analysis using edgeR (R package)</description>
4 4
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>-->
98 echo "Converting PDF figures to PNG" ; 98 echo "Converting PDF figures to PNG" ;
99 99
100 #if $output_MDSplot_logFC: 100 #if $output_MDSplot_logFC:
101 #set $output_MDSplot_logFC_tmp = str($output_MDSplot_logFC)+".png" 101 #set $output_MDSplot_logFC_tmp = str($output_MDSplot_logFC)+".png"
102 102
103 gm convert $output_MDSplot_logFC $output_MDSplot_logFC_tmp ; 103 gm convert $output_MDSplot_logFC png:$output_MDSplot_logFC_tmp ;
104 mv $output_MDSplot_logFC_tmp $output_MDSplot_logFC ; 104 mv $output_MDSplot_logFC_tmp $output_MDSplot_logFC ;
105 #end if 105 #end if
106 106
107 #if $output_MDSplot_bcv: 107 #if $output_MDSplot_bcv:
108 #set $output_MDSplot_bcv_tmp = str($output_MDSplot_bcv)+".png" 108 #set $output_MDSplot_bcv_tmp = str($output_MDSplot_bcv)+".png"
109 109
110 gm convert $output_MDSplot_bcv $output_MDSplot_bcv_tmp ; 110 gm convert $output_MDSplot_bcv png:$output_MDSplot_bcv_tmp ;
111 mv $output_MDSplot_bcv_tmp $output_MDSplot_bcv ; 111 mv $output_MDSplot_bcv_tmp $output_MDSplot_bcv ;
112 #end if 112 #end if
113 113
114 #if $output_BCVplot: 114 #if $output_BCVplot:
115 #set $output_BCVplot_tmp = str($output_BCVplot)+".png" 115 #set $output_BCVplot_tmp = str($output_BCVplot)+".png"
116 116
117 gm convert $output_BCVplot $output_BCVplot_tmp ; 117 gm convert $output_BCVplot png:$output_BCVplot_tmp ;
118 mv $output_BCVplot_tmp $output_BCVplot ; 118 mv $output_BCVplot_tmp $output_BCVplot ;
119 #end if 119 #end if
120 120
121 #if $output_MAplot: 121 #if $output_MAplot:
122 #set $output_MAplot_tmp = str($output_MAplot)+".png" 122 #set $output_MAplot_tmp = str($output_MAplot)+".png"
123 123
124 gm convert $output_MAplot $output_MAplot_tmp ; 124 gm convert $output_MAplot png:$output_MAplot_tmp ;
125 mv $output_MAplot_tmp $output_MAplot ; 125 mv $output_MAplot_tmp $output_MAplot ;
126 #end if 126 #end if
127 127
128 #if $output_PValue_distribution_plot: 128 #if $output_PValue_distribution_plot:
129 #set $output_PValue_distribution_plot_tmp = str($output_PValue_distribution_plot)+".png" 129 #set $output_PValue_distribution_plot_tmp = str($output_PValue_distribution_plot)+".png"
130 130
131 gm convert $output_PValue_distribution_plot $output_PValue_distribution_plot_tmp ; 131 gm convert $output_PValue_distribution_plot png:$output_PValue_distribution_plot_tmp ;
132 mv $output_PValue_distribution_plot_tmp $output_PValue_distribution_plot ; 132 mv $output_PValue_distribution_plot_tmp $output_PValue_distribution_plot ;
133 #end if 133 #end if
134 134
135 #if $output_hierarchical_clustering_plot: 135 #if $output_hierarchical_clustering_plot:
136 #set $output_hierarchical_clustering_plot_tmp = str($output_hierarchical_clustering_plot)+".png" 136 #set $output_hierarchical_clustering_plot_tmp = str($output_hierarchical_clustering_plot)+".png"
137 137
138 gm convert $output_hierarchical_clustering_plot $output_hierarchical_clustering_plot_tmp ; 138 gm convert $output_hierarchical_clustering_plot png:$output_hierarchical_clustering_plot_tmp ;
139 mv $output_hierarchical_clustering_plot_tmp $output_hierarchical_clustering_plot ; 139 mv $output_hierarchical_clustering_plot_tmp $output_hierarchical_clustering_plot ;
140 #end if 140 #end if
141 141
142 #if $output_heatmap_plot: 142 #if $output_heatmap_plot:
143 #set $output_heatmap_plot_tmp = str($output_heatmap_plot)+".png" 143 #set $output_heatmap_plot_tmp = str($output_heatmap_plot)+".png"
144 144
145 gm convert $output_heatmap_plot $output_heatmap_plot_tmp ; 145 gm convert $output_heatmap_plot png:$output_heatmap_plot_tmp ;
146 mv $output_heatmap_plot_tmp $output_heatmap_plot ; 146 mv $output_heatmap_plot_tmp $output_heatmap_plot ;
147 #end if 147 #end if
148 #end if 148 #end if
149 149
150 grep -v 'Calculating library sizes from column' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 150 grep -v 'Calculating library sizes from column' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ;