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comparison idba_tran.xml @ 1:33f00ff1cb22 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 665baeb11498ceef8abb1f1da43fe315d2d75b37"
author iuc
date Tue, 04 Aug 2020 05:51:17 -0400
parents a30d991a3fdd
children 03de4e0f84c2
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0:a30d991a3fdd 1:33f00ff1cb22
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>