diff macros.xml @ 11:7dd841a32245 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit df07890f27c5d18e423ec889eadca82bd7958def

--- a/macros.xml	Sun Feb 13 22:43:45 2022 +0000
+++ b/macros.xml	Sat Oct 01 08:43:22 2022 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">3.6</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">3.7</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">pygenometracks</requirement>
@@ -61,6 +61,27 @@
     <xml name="track_input_link_macro">
         <param name="track_input_link" type="data" format="bed,interval" label="Track file(s) for links" multiple="False"/>
     </xml>
+    <xml name="track_input_fasta_macro">
+        <conditional name="fasta_source">
+            <param name="fasta_source_selector" type="select" label="Choose the source for the fasta to display">
+                <option value="cached">Locally cached</option>
+                <option value="history">History</option>
+            </param>
+            <when value="cached">
+                <param name="fasta_cached" type="select" label="Fasta availables">
+                    <options from_data_table="fasta_indexes">
+                        <validator type="no_options" message="No cached fasta is available"/>
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="fasta_local" type="data" format="fasta" label="Fasta from history"/>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="track_input_maf_macro">
+        <param name="track_input_maf" type="data" format="maf" label="Track file for maf" multiple="False"/>
+    </xml>
     <!-- Common to nearly all tracks: -->
     <xml name="plot_title">
         <param name="title" type="text" optional="true" label="Plot title" multiple="True"/>
@@ -166,6 +187,20 @@
             <when value="none" />
         </conditional>
     </xml>
+    <xml name="backbone_color_bed_macro">
+        <conditional name="backbone_color_bed">
+            <param name="backbone_color_bed_select" type="select" label="Define the color of the backbone:">
+                <option value="manually" selected="True">manually</option>
+                <option value="bed_rgb">From the 9th field</option>
+                <option value="none">No border</option>
+            </param>
+            <when value="manually">
+                <param name="color" type="color" value="#000000" label="Color of the backbone"/>
+            </when>
+            <when value="bed_rgb" />
+            <when value="none" />
+        </conditional>
+    </xml>
     <xml name="bed_advanced_macro">
         <param name="global_max_row" type="boolean" truevalue="true" falsevalue="false" checked="false"
                 label="Global max rows" />
@@ -175,8 +210,17 @@
         <section name ="gtf" title="When using gtf as input" expanded="False">
             <param name="prefered_name" type="text" value="transcript_name" label="attribute to use as label"
                 help="Usually transcript_name or gene_name"/>
-            <param name="merge_transcripts" type="boolean" truevalue="true" falsevalue="false" checked="false"
-                label="Merge all transcripts of each gene in a single entry" />
+            <conditional name="merge_transcripts">
+                <param name="merge_transcripts_select" type="select" label="Merge all transcripts of each gene in a single entry">
+                    <option value="false" selected="True">No</option>
+                    <option value="true">Yes</option>
+                </param>
+                <when value="true">
+                    <param name="merge_overlapping_exons" type="boolean" truevalue="true" falsevalue="false" checked="true"
+                        label="Merge overlapping exons" help="Usually it makes prettier plots" />
+                </when>
+                <when value="false" />
+            </conditional>
         </section>
     </xml>
     <xml name="utr_macro">
@@ -352,4 +396,21 @@
         <option value="magma_r">magma reversed</option>
         <option value="cividis_r">cividis reversed</option>
     </xml>
+    <xml name="links_arcs_triangles_options">
+        <param name="compact_arcs_level" type="select" label="Height of arcs and triangles:">
+            <option value="0" selected="True">default (proportional to distance)</option>
+            <option value="1">compacted (the height is proportional to the square root of the distance)</option>
+            <option value="2">highly compacted (the height is the same for all distances)</option>
+        </param>
+        <param name="use_middle" type="select" label="Coordinates to use" help="Not useful with loops">
+            <option value="false" selected="True">Extremities (start of first and end of second)</option>
+            <option value="true">Center (mean of start and end for each)</option>
+        </param>
+    </xml>
+    <xml name="region2_option">
+        <param name="region2" type="text" label="Region of the genome that should be plotted on the y axis" optional="true"
+            value="" help="The format is chr:start-end, for example chr10:10-500. By default this is the region on the x-axis. Top is start and bottom is end. Use 'Invert the track' if you want the contrary.">
+            <validator type="expression" message="Region should be like chr10:10-500">'^[a-zA-Z0-9_]:\d+-\d+$'</validator>
+        </param>
+    </xml>
 </macros>