Mercurial > repos > galaxyp > pvactools

diff shared_macros.xml @ 0:8184d4998259 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
author galaxyp
date Fri, 12 Dec 2025 16:49:12 +0000
parents
children 747d464670f9
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/shared_macros.xml	Fri Dec 12 16:49:12 2025 +0000
@@ -0,0 +1,49 @@
+<macros>
+    <token name="@TOOL_VERSION@">6.0.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@AA_RE@">[ACDEFGHIKLMNPQRSTVWY]</token>
+    <token name="@PROBLEM_AA_RE@">(@AA_RE@+|@AA_RE@:-?\d+)</token>
+    <token name="@PROBLEM_AA_ARG_RE@">@PROBLEM_AA_RE@(,@PROBLEM_AA_RE@)*</token>
+    <token name="@PREPARE_ALLELES_INPUT@"><![CDATA[
+        #if $alleles.allelesrc == 'entry'
+            #set $alleles_input = ''
+            #if $alleles.allele_text != ''
+                #set $alleles_input = ','.join(str($alleles.allele_text).strip().split())
+            #end if
+
+            #if $alleles.allele_select != 'None'
+                #set $select_alleles = ','.join(str($alleles.allele_select).strip().split())
+                #if $alleles_input == ''
+                    #set $alleles_input = $select_alleles
+                #else
+                    #set $alleles_input = ','.join([$alleles_input, $select_alleles])
+                #end if
+            #end if
+        #end if
+    ]]></token>
+    <xml name="allele_inputs">
+        <conditional name="alleles">
+           <param name="allelesrc" type="select" label="Alleles">
+               <option value="history">From history</option>
+               <option value="entry">Entered</option>
+           </param>
+           <when value="history">
+               <param name="allele_file" type="data" format="txt,tabular,tsv" label="Alleles file">
+                   <help>The dataset should have one allele per line.</help>
+               </param>
+           </when>
+           <when value="entry">
+               <param name="allele_text" type="text" label="Alleles" optional="true">
+                   <help>Enter alleles separated by white space.</help>
+               </param>
+               <expand macro="allele_list" />
+           </when>
+        </conditional>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1158/2326-6066.CIR-19-0401</citation>
+            <yield />
+        </citations>
+    </xml>
+</macros>