Mercurial > repos > iuc > idba_tran
comparison idba_tran.xml @ 1:33f00ff1cb22 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 665baeb11498ceef8abb1f1da43fe315d2d75b37"
author | iuc |
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date | Tue, 04 Aug 2020 05:51:17 -0400 |
parents | a30d991a3fdd |
children | 03de4e0f84c2 |
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0:a30d991a3fdd | 1:33f00ff1cb22 |
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1 <tool id="idba_tran" name="IDBA-TRAN" version="@IDBA_VERSION@"> | 1 <tool id="idba_tran" name="IDBA-TRAN" version="@IDBA_VERSION@+galaxy0"> |
2 <description> | 2 <description> |
3 Iterative de Bruijn Graph Assembler for transcriptome data | 3 Iterative de Bruijn Graph Assembler for transcriptome data |
4 </description> | 4 </description> |
5 <macros> | 5 <macros> |
6 <import>macros.xml</import> | 6 <import>macros.xml</import> |
26 <param argument="--max_isoforms" type="integer" value="3" label="Maximum number of isoforms"/> | 26 <param argument="--max_isoforms" type="integer" value="3" label="Maximum number of isoforms"/> |
27 <param argument="--max_component_size" type="integer" value="30" label="Maximum size of component"/> | 27 <param argument="--max_component_size" type="integer" value="30" label="Maximum size of component"/> |
28 <expand macro="other_options"/> | 28 <expand macro="other_options"/> |
29 </inputs> | 29 </inputs> |
30 <outputs> | 30 <outputs> |
31 <data name="output" from_work_dir="out/scaffold.fa" format="fasta"/> | 31 <data name="output" from_work_dir="out/contig.fa" format="fasta"/> |
32 </outputs> | 32 </outputs> |
33 <tests> | 33 <tests> |
34 <!-- basic test + tool specific defaults --> | 34 <!-- basic test + tool specific defaults --> |
35 <test> | 35 <test> |
36 <param name="read" value="merged.fa" ftype="fasta"/> | 36 <param name="read" value="merged.fa" ftype="fasta"/> |
39 <has_text text="--step 10" /> | 39 <has_text text="--step 10" /> |
40 <has_text text="--min_transcript 300" /> | 40 <has_text text="--min_transcript 300" /> |
41 <has_text text="--max_isoforms 3" /> | 41 <has_text text="--max_isoforms 3" /> |
42 <has_text text="--max_component_size 30" /> | 42 <has_text text="--max_component_size 30" /> |
43 </assert_command> | 43 </assert_command> |
44 <output name="output" file="out/scaffold.fa" ftype="fasta" compare="sim_size"/> | 44 <output name="output" file="out/contig.fa" ftype="fasta" lines_diff="2"/> |
45 </test> | 45 </test> |
46 <!-- tool specific parameters --> | 46 <!-- tool specific parameters --> |
47 <test> | 47 <test> |
48 <param name="read" value="merged.fa" ftype="fasta"/> | 48 <param name="read" value="merged.fa" ftype="fasta"/> |
49 <param name="min_transcript" value="299"/> | 49 <param name="min_transcript" value="299"/> |
52 <assert_command> | 52 <assert_command> |
53 <has_text text="--min_transcript 299" /> | 53 <has_text text="--min_transcript 299" /> |
54 <has_text text="--max_isoforms 2" /> | 54 <has_text text="--max_isoforms 2" /> |
55 <has_text text="--max_component_size 29" /> | 55 <has_text text="--max_component_size 29" /> |
56 </assert_command> | 56 </assert_command> |
57 <output name="output" file="out/scaffold.fa" ftype="fasta" compare="sim_size"/> | 57 <output name="output" file="out/contig.fa" ftype="fasta" lines_diff="2"/> |
58 </test> | 58 </test> |
59 </tests> | 59 </tests> |
60 <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."/> | 60 <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."/> |
61 <expand macro="citations"> | 61 <expand macro="citations"> |
62 <citation type="doi">10.1093/bioinformatics/btt219</citation> | 62 <citation type="doi">10.1093/bioinformatics/btt219</citation> |