changeset 1:33f00ff1cb22 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 665baeb11498ceef8abb1f1da43fe315d2d75b37"

--- a/idba_tran.xml	Mon Aug 05 15:58:44 2019 -0400
+++ b/idba_tran.xml	Tue Aug 04 05:51:17 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="idba_tran" name="IDBA-TRAN" version="@IDBA_VERSION@">
+<tool id="idba_tran" name="IDBA-TRAN" version="@IDBA_VERSION@+galaxy0">
     <description>
         Iterative de Bruijn Graph Assembler for transcriptome data
     </description>
@@ -28,7 +28,7 @@
         <expand macro="other_options"/>
     </inputs>
     <outputs>
-        <data name="output" from_work_dir="out/scaffold.fa" format="fasta"/>
+        <data name="output" from_work_dir="out/contig.fa" format="fasta"/>
     </outputs>
     <tests>
         <!-- basic test + tool specific defaults -->
@@ -41,7 +41,7 @@
                 <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"/>
+            <output name="output" file="out/contig.fa" ftype="fasta" lines_diff="2"/>
         </test>
         <!-- tool specific parameters -->
         <test>
@@ -54,7 +54,7 @@
                 <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"/>
+            <output name="output" file="out/contig.fa" ftype="fasta" lines_diff="2"/>
         </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."/>

--- a/test-data/out/contig.fa	Mon Aug 05 15:58:44 2019 -0400
+++ b/test-data/out/contig.fa	Tue Aug 04 05:51:17 2020 -0400
@@ -1,2 +1,2 @@
->contig-100_0 length_749 read_count_0
-GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA
+>contig-60_0 length_749 read_count_302
+TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATATACCGACGACTCACCACTAACGACAATAACGCTGGTATAACTATATCCTGTGCGCAAGGAAGTAACCTGCGACCCATCTGCAAGCGCGTTTTTC