diff pretext_graph.xml @ 0:75b4a2298714 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit c03782a5d213b2d272c0cbe9af2b7196fab2dc1c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pretext_graph.xml	Tue Feb 13 21:59:26 2024 +0000
@@ -0,0 +1,63 @@
+<tool id="pretext_graph" name="Pretextgraph"  version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+    <description>Embed bedgraph formatted data inside a Pretext contact map.</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.0.6</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">pretextgraph</requirement>
+        <requirement type="package" version="377"> ucsc-bigwigtobedgraph</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        cp '$pretext' input.pretext &&
+        #if $input.is_of_type("bedgraph"):
+            cat '$input' | 
+        #else if $input.is_of_type("bigwig"):
+            ln -s '$input' input.bigwig &&
+            bigWigToBedGraph input.bigwig /dev/stdout |
+        #end if
+        PretextGraph -i input.pretext
+        #if $name:
+            -n '$name'
+        #end if
+        -o output.pretext
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="bigwig, bedgraph" label="Input bigwig or bedgraph file"/>
+        <param name="pretext" type="data" format="pretext" label="Pretext file" help="Sequence names in the Pretext file must match sequence names in the bedgraph data; although relative sort order is unimportant."/>
+        <param name="name" type="text" label="Label for the graph" optional="true"/>
+    </inputs>
+    <outputs>
+        <data name="graph_out" format="pretext" from_work_dir="output.pretext" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <!-- BIGWIG TEST -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input_graph.bw" ftype="bigwig"/>
+            <param name="pretext" value="input_graph.pretext" ftype="pretext"/>
+            <param name="name" value="testing"/>
+            <output name="graph_out" file="output_4.pretext"/>
+        </test>
+            <!-- BEDGRAPH TEST -->
+            <test expect_num_outputs="1">
+                <param name="input" value="input_graph.bgr" ftype="bedgraph"/>
+                <param name="pretext" value="input_graph.pretext" ftype="pretext"/>
+                <param name="name" value="testing_2"/>
+                <output name="graph_out" file="output_5.pretext"/>
+            </test>
+    </tests>
+    <help><![CDATA[
+        Adds additional data onto existing pretextmap files.
+        Input Pretext file acts as a foundation for additional data to be added onto. 
+        Sequence names in the Pretext file must match sequence names in the bedgraph data; although relative sort order is unimportant.
+        The chosen name acts as a lable on the graph.
+    ]]></help>
+        <citations>
+            <citation type="bibtex">
+                @misc{Harry_et_al,
+                Author={Harry, E},
+                title={Paired REad TEXTure Graph: Embeds bedgraph data into Pretext contact maps.},
+                url = {https://github.com/wtsi-hpag/PretextGraph},}
+            </citation>
+        </citations>
+</tool>