Mercurial > repos > jjohnson > arriba

diff arriba_download_reference.xml @ 5:005b200c8841 draft

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"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
author jjohnson
date Sun, 10 Oct 2021 13:00:45 +0000
parents 77021ad5037d
children 8c4c97fd0555
line wrap: on
line diff
--- a/arriba_download_reference.xml	Sat Oct 09 15:41:49 2021 +0000
+++ b/arriba_download_reference.xml	Sun Oct 10 13:00:45 2021 +0000
@@ -9,19 +9,19 @@
     echo $arriba_reference_name > '$star_index' &&
     BASE_DIR=\$(dirname \$(dirname `which arriba`)) &&
     REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` &&
+    #if $is_test != 'yes'
     \$REF_SCRIPT '$arriba_reference_name' &&
     cp *.fa*  '$genome_fasta' &&
     cp *.gtf*  '$genome_gtf' &&
     mv STAR_index_* '$star_index.extra_files_path'
+    #else
+    [[ -x \$REF_SCRIPT ]]
+    #end if
     ]]></command>
     <inputs>
+        <param name="is_test" type="hidden" value="no"/>
         <param name="arriba_reference_name" type="select" label="Select reference">
-            <option value="GRCh37+ENSEMBL87">GRCh37+ENSEMBL87</option>
-            <option value="GRCh37+GENCODE19">GRCh37+GENCODE19</option>
-            <option value="GRCh37+RefSeq">GRCh37+RefSeq</option>
-            <option value="GRCh37viral+ENSEMBL87">GRCh37viral+ENSEMBL87</option>
-            <option value="GRCh37viral+GENCODE19">GRCh37viral+GENCODE19</option>
-            <option value="GRCh37viral+RefSeq">GRCh37viral+RefSeq</option>
+
             <option value="GRCh38+ENSEMBL93">GRCh38+ENSEMBL93</option>
             <option value="GRCh38+GENCODE28">GRCh38+GENCODE28</option>
             <option value="GRCh38+RefSeq">GRCh38+RefSeq</option>
@@ -32,18 +32,24 @@
             <option value="GRCm38+RefSeq">GRCm38+RefSeq</option>
             <option value="GRCm38viral+GENCODEM25">GRCm38viral+GENCODEM25</option>
             <option value="GRCm38viral+RefSeq">GRCm38viral+RefSeq</option>
+            <option value="hg38+ENSEMBL93">hg38+ENSEMBL93</option>
+            <option value="hg38+GENCODE28">hg38+GENCODE28</option>
+            <option value="hg38+RefSeq">hg38+RefSeq</option>
+            <option value="hg38viral+ENSEMBL93">hg38viral+ENSEMBL93</option>
+            <option value="hg38viral+GENCODE28">hg38viral+GENCODE28</option>
+            <option value="hg38viral+RefSeq">hg38viral+RefSeq</option>
+            <option value="GRCh37+ENSEMBL87">GRCh37+ENSEMBL87</option>
+            <option value="GRCh37+GENCODE19">GRCh37+GENCODE19</option>
+            <option value="GRCh37+RefSeq">GRCh37+RefSeq</option>
+            <option value="GRCh37viral+ENSEMBL87">GRCh37viral+ENSEMBL87</option>
+            <option value="GRCh37viral+GENCODE19">GRCh37viral+GENCODE19</option>
+            <option value="GRCh37viral+RefSeq">GRCh37viral+RefSeq</option>
             <option value="hg19+ENSEMBL87">hg19+ENSEMBL87</option>
             <option value="hg19+GENCODE19">hg19+GENCODE19</option>
             <option value="hg19+RefSeq">hg19+RefSeq</option>
             <option value="hg19viral+ENSEMBL87">hg19viral+ENSEMBL87</option>
             <option value="hg19viral+GENCODE19">hg19viral+GENCODE19</option>
             <option value="hg19viral+RefSeq">hg19viral+RefSeq</option>
-            <option value="hg38+ENSEMBL93">hg38+ENSEMBL93</option>
-            <option value="hg38+GENCODE28">hg38+GENCODE28</option>
-            <option value="hg38+RefSeq">hg38+RefSeq</option>
-            <option value="hg38viral+ENSEMBL93">hg38viral+ENSEMBL93</option>
-            <option value="hg38viral+GENCODE28">hg38viral+GENCODE28</option>
-            <option value="hg38viral+RefSeq">hg38viral+RefSeq</option>
             <option value="hs37d5+ENSEMBL87">hs37d5+ENSEMBL87</option>
             <option value="hs37d5+GENCODE19">hs37d5+GENCODE19</option>
             <option value="hs37d5+RefSeq">hs37d5+RefSeq</option>
@@ -61,12 +67,42 @@
         <data name="genome_gtf" format="gtf" label="${tool.name} ${arriba_reference_name} GTF"/>
         <data name="star_index" format="txt" label="${tool.name} ${arriba_reference_name} STAR index"/>
     </outputs>
+    <tests>
+        <!-- Downloading a genome and annotation plus build a STAR index requires too many resources for testing. 
+              Just test that we can locate the script. -->
+        <test>
+            <param name="is_test" value="yes"/>
+            <param name="arriba_reference_name" value="GRCh38+ENSEMBL93"/>
+            <output name="star_index">
+                <assert_contents>
+                    <has_text text="GRCh38+ENSEMBL93"/>
+                </assert_contents>
+            </output>
+
+        </test>
+    </tests>
     <help><![CDATA[
-** Arriba **
+** Arriba Reference **
 
 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 Reference** downloads a genome sequence fasta and its related annoation GTF, and then build a STAR index for the RNA STAR aligner.  
+
+These datasets will be added to your Galaxy history:
+
+    - genome assembly fasta 
+    - genome annotation GTF 
+    - STAR index
+
+See Arriba manual pages:
+
+  - https://arriba.readthedocs.io/en/latest/workflow/
+  - https://arriba.readthedocs.io/en/latest/input-files/
+
+
+**NOTE:** This is a resource intensive process, so the results should be copies to new histories as needed rather than running this in each workflow.
+
 .. _Arriba: https://arriba.readthedocs.io/en/latest/
 
 ]]></help>