diff idba_tran.xml @ 0:a30d991a3fdd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/idba_tran.xml	Mon Aug 05 15:58:44 2019 -0400
@@ -0,0 +1,64 @@
+<tool id="idba_tran" name="IDBA-TRAN" version="@IDBA_VERSION@">
+    <description>
+        Iterative de Bruijn Graph Assembler for transcriptome data
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+    idba_tran
+
+    @MAIN_INPUT@
+    @KMER_OPTIONS@
+    @FILTER_OPTIONS@
+    --min_transcript $min_transcript
+    --max_isoforms $max_isoforms
+    --max_component_size $max_component_size
+    @OTHER_OPTIONS@
+    @THREADS@
+    ]]></command>
+    <inputs>
+        <expand macro="main_input"/>
+        <expand macro="kmer_options" maxk_default="60" step_default="10"/>
+        <expand macro="filter_options"/>
+        <param argument="--min_transcript" type="integer" value="300" label="Minimum size of transcript"/>
+        <param argument="--max_isoforms" type="integer" value="3" label="Maximum number of isoforms"/>
+        <param argument="--max_component_size" type="integer" value="30" label="Maximum size of component"/>
+        <expand macro="other_options"/>
+    </inputs>
+    <outputs>
+        <data name="output" from_work_dir="out/scaffold.fa" format="fasta"/>
+    </outputs>
+    <tests>
+        <!-- basic test + tool specific defaults -->
+        <test>
+            <param name="read" value="merged.fa" ftype="fasta"/>
+            <assert_command>
+                <has_text text="--maxk 60" />
+                <has_text text="--step 10" />
+                <has_text text="--min_transcript 300" />
+                <has_text text="--max_isoforms 3" />
+                <has_text text="--max_component_size 30" />
+            </assert_command>
+            <output name="output" file="out/scaffold.fa" ftype="fasta" compare="sim_size"/>
+        </test>
+        <!-- tool specific parameters -->
+        <test>
+            <param name="read" value="merged.fa" ftype="fasta"/>
+            <param name="min_transcript" value="299"/>
+            <param name="max_isoforms" value="2"/>
+            <param name="max_component_size" value="29"/>
+            <assert_command>
+                <has_text text="--min_transcript 299" />
+                <has_text text="--max_isoforms 2" />
+                <has_text text="--max_component_size 29" />
+            </assert_command>
+            <output name="output" file="out/scaffold.fa" ftype="fasta" compare="sim_size"/>
+        </test>
+    </tests>
+    <expand macro="help" more_help="IDBA-Tran is an iterative De Bruijn Graph De Novo short read assembler for transcriptome. It is purely de novo assembler based on only RNA sequencing reads. IDBA-Tran uses local assembly to reconstructing missing k-mers in low-expressed transcripts and then employs progressive cutoff on contigs to seperate the graph into components. Each component corresponds to one gene in most cases and contains not many transcripts. A heuristic algorithm based on pair-end reads is then used to find the isoforms."/>
+    <expand macro="citations">
+       <citation type="doi">10.1093/bioinformatics/btt219</citation>
+    </expand>
+</tool>