diff hicInterIntraTAD.xml @ 0:55b013e59018 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicInterIntraTAD.xml	Wed Oct 18 17:02:07 2023 +0000
@@ -0,0 +1,79 @@
+<tool id="hicexplorer_hicinterintratad" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>computes the ratio of inter TAD-scores vs. intra TADs</description>
+    <macros>
+        <token name="@BINARY@">hicInterIntraTAD</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
+
+       @BINARY@
+            --matrix 'matrix.$matrix_h5_cooler.ext'
+            --tadDomains '$tadDomains'
+
+            #if $fontSize:
+                --fontSize $fontSize
+            #end if
+
+            #if $dpi:
+                --dpi $dpi
+            #end if
+
+            --outFileName output_interintra.txt
+            --outFileNameRatioPlot plot.$image_file_format
+            --threads @THREADS@
+
+            && mv plot.$image_file_format plot
+            
+    ]]>    </command>
+    <inputs>
+        <expand macro="matrix_h5_cooler_macro" />
+        <param name="tadDomains" type="data" format="bed" label="Bed file with TAD domains coordinates" help="Bed file with domains coordinates: instead of evaluating the distance vs. Hi-C counts for intra chromosomal counts, compute it for intra-domains." />
+
+        <expand macro="dpi" />
+        <param name="fontSize" type="integer" min="5" optional="True" label="Font size" help="Font size for the plot"/>
+        
+        <param name="image_file_format" type="select" label="Image output format">
+            <option value="png" selected="True">png</option>
+            <option value="svg">svg</option>
+            <option value="pdf">pdf</option>
+        </param>
+        
+    </inputs>
+    <outputs>
+       <data name='output_txt' from_work_dir='output_interintra.txt' format='txt' label='Intra Inter TAD ratios'/>
+
+       <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'>
+            <change_format>
+                <when input="image_file_format" value="svg" format="svg" />
+                <when input="image_file_format" value="pdf" format="pdf" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix_h5_cooler" value="hicInterIntraTAD/matrix.cool" />
+            <param name="tadDomains" value="hicInterIntraTAD/untreated_R1_domains_chr1_chr2.bed" />
+            
+            <output name="output_txt" file="hicInterIntraTAD/output.txt" ftype="txt" />
+            
+            <output name="output_plot" file="hicInterIntraTAD/plot.png" ftype="png" />
+            
+        </test>
+      
+    </tests>
+    <help><![CDATA[
+
+Calculate the ratio of inter-TAD contacts vs intra-TADs
+=======================================================
+
+Toplogical domains (TADs) are large mainly self-interacting domains. Chromatin interactions occur with higher frequency within a TAD as between TADs. 
+This tool supports to compute the ratio of contacts of a TAD (intra-TAD) with the contacts outside of it (inter-TAD).
+
+For more information about HiCExplorer please consider our documentation on readthedocs.io_
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+]]>    </help>
+    <expand macro="citations" />
+</tool>