Mercurial > repos > iuc > fasta_nucleotide_color_plot

changeset 3:e4b5401adcec draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot commit ea2c53b2c83e61350bf471981d850fa061bf5512
author iuc
date Fri, 16 Jun 2017 11:58:18 -0400
parents 0fba45ac3987
children
files fasta_nucleotide_color_plot.xml
diffstat 1 files changed, 32 insertions(+), 34 deletions(-) [+]
line wrap: on
line diff
--- a/fasta_nucleotide_color_plot.xml	Fri Jan 13 10:19:56 2017 -0500
+++ b/fasta_nucleotide_color_plot.xml	Fri Jun 16 11:58:18 2017 -0400
@@ -6,40 +6,38 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <command>
-        <![CDATA[
-            java -jar $__tool_directory__/FourColorPlot.jar
-            -f "$input"
-            -h $pixel_height
-            -w $pixel_width
-            #if str($a_select_color_cond.a_select_color) == "a_rgb":
-                -A "$a_select_color_cond.a_rgb"
-            #else:
-                -A $a_select_color_cond.color_a
-            #end if
-            #if str($t_select_color_cond.t_select_color) == "t_rgb":
-                -T "$t_select_color_cond.t_rgb"
-            #else
-                -T $t_select_color_cond.color_t
-            #end if
-            #if str($g_select_color_cond.g_select_color) == "g_rgb":
-                -G "$g_select_color_cond.g_rgb"
-            #else
-                -G $g_select_color_cond.color_g
-            #end if
-            #if str($c_select_color_cond.c_select_color) == "c_rgb":
-                -C "$c_select_color_cond.c_rgb"
-            #else
-                -C $c_select_color_cond.color_c
-            #end if
-            #if str($n_select_color_cond.n_select_color) == "n_rgb":
-                -N "$n_select_color_cond.n_rgb"
-            #else
-                -N $n_select_color_cond.color_n
-            #end if
-            -o "$output" 1>/dev/null
-        ]]>
-    </command>
+    <command detect_errors="exit_code"><![CDATA[
+java -jar '$__tool_directory__/FourColorPlot.jar'
+-f '$input'
+-h $pixel_height
+-w $pixel_width
+#if str($a_select_color_cond.a_select_color) == "a_rgb":
+    -A '$a_select_color_cond.a_rgb'
+#else:
+    -A $a_select_color_cond.color_a
+#end if
+#if str($t_select_color_cond.t_select_color) == "t_rgb":
+    -T '$t_select_color_cond.t_rgb'
+#else
+    -T $t_select_color_cond.color_t
+#end if
+#if str($g_select_color_cond.g_select_color) == "g_rgb":
+    -G '$g_select_color_cond.g_rgb'
+#else
+    -G $g_select_color_cond.color_g
+#end if
+#if str($c_select_color_cond.c_select_color) == "c_rgb":
+    -C '$c_select_color_cond.c_rgb'
+#else
+    -C $c_select_color_cond.color_c
+#end if
+#if str($n_select_color_cond.n_select_color) == "n_rgb":
+    -N '$n_select_color_cond.n_rgb'
+#else
+    -N $n_select_color_cond.color_n
+#end if
+-o '$output' 1>/dev/null
+    ]]></command>
     <inputs>
         <param name="input" type="data" format="fasta" label="FASTA file" />
         <param name="pixel_height" type="integer" value="2" min="1" label="Pixel height per nucleotide" />