Mercurial > repos > fubar > jbrowse2

diff macros.xml @ 93:4c517a0041a8 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
author fubar
date Wed, 24 Apr 2024 02:29:32 +0000
parents 408781c080fc
children 74074746ccd8
line wrap: on
line diff
--- a/macros.xml	Sun Apr 21 04:42:29 2024 +0000
+++ b/macros.xml	Wed Apr 24 02:29:32 2024 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">2.10.1</token>
+    <token name="@TOOL_VERSION@">2.11.0</token>
     <xml name = "edamInc">
         <edam_topics>
             <edam_topic>topic_3307</edam_topic>
@@ -20,7 +20,8 @@
             <requirement type="package" version="6.0.1">pyyaml</requirement>
             <requirement type="package" version="1.11">tabix</requirement>
             <requirement type="package" version="4.6.0">findutils</requirement>
-            <requirement type="package" version="0.0.8">hictk</requirement>
+            <requirement type="package" version="0.0.12-0">hictk</requirement>
+            <requirement type="package" version="3.0">zip</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -539,51 +540,51 @@
 
     <xml name="input_conditional" token_label="Track Data" token_format="data">
         <conditional name="useuri">
-                <param name="insource" type="select" label="Define track data as a history file or an internet URI"
-                    help="A public URI implies that all the associated tabix files are also in place. They are created for history files">
-                    <option value="history" selected="true">Track data from a history file</option>
-                    <option value="uri" >Tabix data URI - index files must be available at corresponding URI</option>
+            <param name="insource" type="select" label="Define track data as a history file or an internet URI"
+                help="A public URI implies that all the associated tabix files are also in place. They are created for history files">
+                <option value="history" selected="true">Track data from a history file</option>
+                <option value="uri" >Tabix data URI - index files must be available at corresponding URI</option>
+            </param>
+            <when value="history">
+                <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" />
+            </when>
+            <when value="uri">
+                <param label="@LABEL@" name="annouri"  type="text" />
+                <param label="Short name for track display" name="annoname" type="text" >
+                    <sanitizer invalid_char="_">
+                    <valid initial="string.printable" >
+                        <remove value="'" />
+                    </valid>
+                    </sanitizer>
                 </param>
-                <when value="history">
-                       <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" />
-                </when>
-                <when value="uri">
-                       <param label="@LABEL@" name="annouri"  type="text" />
-                       <param label="Short name for track display" name="annoname" type="text" >
-                             <sanitizer invalid_char="_">
+            </when>
+        </conditional>
+    </xml>
+    <xml name="pafref_conditional" token_label="Track Data" token_format="data">
+        <conditional name="pafuseuri">
+            <param name="insource" type="select" label="PAF reference data from a history file or an internet URI?"
+                help="Multiple references can be used for mashmap PAF. A URI source requires all the associated tabix index files to be in place.">
+                <option value="history" selected="true">PAF reference comparison genome from a history file</option>
+                <option value="uri">PAF reference comparison genome tabix .gz URI with index files at the corresponding URIs</option>
+            </param>
+            <when value="history">
+                    <param label="@LABEL@" format="@FORMAT@" name="annotation"  type="data"
+                        help="Add all PAF reference comparison genomes used to make the PAF" multiple="true" />
+            </when>
+            <when value="uri">
+                <repeat name="refuri" title="PAF reference comparison genome URI" min="1">
+                    <param label="@LABEL@" name="annotation"  type="text" />
+                    <param label="Short name for this reference" name="annoname" type="text" help="Short names take less track space">
+                            <sanitizer invalid_char="_">
                                 <valid initial="string.printable" >
                                     <remove value="'" />
                                 </valid>
-                              </sanitizer>
-                        </param>
-                </when>
-            </conditional>
-     </xml>
-    <xml name="pafref_conditional" token_label="Track Data" token_format="data">
-        <conditional name="pafuseuri">
-                <param name="insource" type="select" label="PAF reference data from a history file or an internet URI?"
-                    help="Multiple references can be used for mashmap PAF. A URI source requires all the associated tabix index files to be in place.">
-                    <option value="history" selected="true">PAF reference comparison genome from a history file</option>
-                    <option value="uri">PAF reference comparison genome tabix .gz URI with index files at the corresponding URIs</option>
-                </param>
-                <when value="history">
-                       <param label="@LABEL@" format="@FORMAT@" name="annotation"  type="data"
-                          help="Add all PAF reference comparison genomes used to make the PAF" multiple="true" />
-                </when>
-                <when value="uri">
-                    <repeat name="refuri" title="PAF reference comparison genome URI" min="1">
-                       <param label="@LABEL@" name="annotation"  type="text" />
-                       <param label="Short name for this reference" name="annoname" type="text" help="Short names take less track space">
-                             <sanitizer invalid_char="_">
-                                <valid initial="string.printable" >
-                                    <remove value="'" />
-                                </valid>
-                              </sanitizer>
-                        </param>
-                    </repeat>
-                </when>
-            </conditional>
-     </xml>
+                            </sanitizer>
+                    </param>
+                </repeat>
+            </when>
+        </conditional>
+    </xml>
     <xml name="citations">
         <citations>
         <citation type="doi">10.1186/s13059-016-0924-1</citation>