Mercurial > repos > jackcurragh > ribogalaxy_create_ribosome_profile

changeset 5:4d69f7428243 draft

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Uploaded
author jackcurragh
date Wed, 18 May 2022 12:02:46 +0000
parents 49e8fcbaaa72
children 8f8affaa5eb4
files create_ribosome_profile/create_ribosome_profile.xml
diffstat 1 files changed, 18 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/create_ribosome_profile/create_ribosome_profile.xml	Wed May 18 11:57:34 2022 +0000
+++ b/create_ribosome_profile/create_ribosome_profile.xml	Wed May 18 12:02:46 2022 +0000
@@ -12,23 +12,25 @@
             #end if
     </command>
     <inputs>
-        <param name="input1" type="data" format="bam" label="BAM file to process"/>
-        <param name="input2" type="integer" value="15" label="Offset to use" help="Use 15 for elongating ribosomes, 12 for initiating and 0 form RNA-seq reads"/>
-        <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?">
-            <option value="builtin">Use a built-in FASTA</option>
-            <option value="history">Use one from the history</option>
-        </param>
-        <when value="builtin">
-            <param name="input1_builtin" type="select" format="fasta" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team">
-                <options from_data_table="builtin_fastas">
-                    <filter type="sort_by" column="2" />
-                    <validator type="no_options" message="No built-ins are available" />
-                </options>
+        <conditional name="refGenomeSource">
+            <param name="input1" type="data" format="bam" label="BAM file to process"/>
+            <param name="input2" type="integer" value="15" label="Offset to use" help="Use 15 for elongating ribosomes, 12 for initiating and 0 form RNA-seq reads"/>
+            <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?">
+                <option value="builtin">Use a built-in FASTA</option>
+                <option value="history">Use one from the history</option>
             </param>
-        </when>
-        <when value="history">
-            <param name="input1_file" type="data" format="fasta" label="FASTA File" />
-        </when>
+            <when value="builtin">
+                <param name="input1_builtin" type="select" format="fasta" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team">
+                    <options from_data_table="builtin_fastas">
+                        <filter type="sort_by" column="2" />
+                        <validator type="no_options" message="No built-ins are available" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="input1_file" type="data" format="fasta" label="FASTA File" />
+            </when>
+        </conditional>
         <param name="input3" type="data" format="fasta" label="FASTA file to which the reads were aligned"/>
         <param name="input4" type="select" label="Approach" help ="Use Offset for RNase and Weight for MNase">
             <option value="offset" selected="true">Use offset approach</option>