diff arriba_get_filters.xml @ 2:7420753b0671 draft

"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/arriba_get_filters.xml	Fri Oct 08 19:23:48 2021 +0000
@@ -0,0 +1,52 @@
+<tool id="arriba_get_filters" name="Arriba Get Filters" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
+    <description>to history</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+    BASE_DIR=\$(dirname \$(dirname `which arriba`)) &&
+    REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` &&
+    REF_DIR=\$(dirname \$REF_SCRIPT) &&
+    REF_NAME=${arriba_reference_name.split('+')[0].replace('viral','')} &&
+    echo \$REF_NAME &&
+    cp `find \$REF_DIR -name 'blacklist_*' | grep -i \$REF_NAME` '$blacklist' && 
+    cp `find \$REF_DIR -name 'known_fusions_*' | grep -i \$REF_NAME` '$known_fusions' &&
+    cp `find \$REF_DIR -name 'protein_domains_*' | grep -i \$REF_NAME` '$protein_domains' &&
+    cp `find \$REF_DIR -name 'cytobands_*' | grep -i \$REF_NAME` '$cytobands'
+    #*
+    cp "\$REF_DIR/blacklist_*${arriba_reference_name}*" '$blacklist' &&
+    cp "\$REF_DIR/known_fusions_*${arriba_reference_name}*" '$known_fusions' &&
+    cp "\$REF_DIR/protein_domains_*${arriba_reference_name}*" '$protein_domains' &&
+    cp "\$REF_DIR/cytobands_*${arriba_reference_name}*" '$cytobands'
+    *#
+    ]]></command>
+    <inputs>
+        <param name="arriba_reference_name" type="text" label="Select reference">
+            <help>GRCh38 GRCh37 hg38 hg19 GRCm38 mm10</help>
+            <option value="GRCh38">GRCh38</option>
+            <option value="GRCh37">GRCh37</option>
+            <option value="hg38">hg38</option>
+            <option value="hg19">hg19</option>
+            <option value="GRCm38">GRCm38</option>
+            <option value="mm10">mm10</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="blacklist" format="tabular" label="${tool.name} ${arriba_reference_name} blacklist"/>
+        <data name="known_fusions" format="tabular" label="${tool.name} ${arriba_reference_name} known_fusions"/>
+        <data name="protein_domains" format="tabular" label="${tool.name} ${arriba_reference_name} protein_domains"/>
+        <data name="cytobands" format="tabular" label="${tool.name} ${arriba_reference_name} cytobands"/>
+    </outputs>
+    <help><![CDATA[
+** Arriba **
+
+Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions.
+It is based on chimeric alignments found by the STAR RNA-Seq aligner.
+
+.. _Arriba: https://arriba.readthedocs.io/en/latest/
+
+]]></help>
+    <expand macro="citations" />
+</tool>