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Update filter_assembly.xml
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cberthelier authored Oct 7, 2024
1 parent 836e357 commit 1f3dab0
Showing 1 changed file with 11 additions and 27 deletions.
38 changes: 11 additions & 27 deletions galaxy_wrappers/01_Filter_Assemblies/filter_assembly.xml
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<tool name="Filter assemblies" id="filter_assemblies" version="2.0.3">
<tool name="Filter assemblies" id="filter_assemblies" version="2.0.4">

<description>
Filter the outputs of Velvet or Trinity assemblies
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<requirements>
<expand macro="python_required" />
<requirement type="package" version="0.0.14">fastx_toolkit</requirement>
<requirement type="package" version="10.2011">cap3</requirement>
</requirements>

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#end for
#set $infiles = $infiles[:-1]
ln -s '$__tool_directory__/scripts/S02a_remove_redondancy_from_velvet_oases.py' . &&
ln -s '$__tool_directory__/scripts/S02b_format_fasta_name_trinity.py' . &&
ln -s '$__tool_directory__/scripts/S03_choose_one_variants_per_locus_trinity.py' . &&
ln -s '$__tool_directory__/scripts/S04_find_orf.py' . &&
ln -s '$__tool_directory__/scripts/S05_filter.py' . &&
python '$__tool_directory__/scripts/S01_script_to_choose.py'
'$infiles'
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**Description**
This tool reformats Velvet Oases or Trinity assemblies for the AdaptSearch galaxy suite and selects only one variant per gene according to its length and quality check.
This tool runs the CAP3 software on assembly FASTA data, merge singlets and contigs and then reformat headers to allow any assembly tools.
---------
**Input format**
(1) Sequences are in the sequential format:
Sequences are in the FASTA format:
| >seqname1
| AAAGAGAGACCACATGTCAGTAGC -on one or several lines -
Expand All @@ -121,18 +114,6 @@ This tool reformats Velvet Oases or Trinity assemblies for the AdaptSearch galax
| etc ...
|
2) The file name should begin with a two letter abbreviation of the species name (for isntance, 'Ap' if the species is Alvinella pompejana).
**For Velvet Oases assemblies input**
The headers must be as follow : *>Locus_i_Transcript_i/j_Confidence_x.xxx_Length_N* where i is the locus number, j the transcript variant among all versions of the transcript, x.xxx the confidence value and N the length.
**For Trinity assemblies inputs**
The headers must be as follow : *>cj_gj_ij Len=j path=[j:0-j]* where all the j are integers (locus number, transcript variant, length, position...)
**The tool handles the case if input files come from both assemblers (there is no need for input files to be exclusively from one or another assembler).**
---------
**Parameters**
Expand All @@ -150,11 +131,9 @@ This tool reformats Velvet Oases or Trinity assemblies for the AdaptSearch galax
**Steps**:
The tool:
1) Modifies the sequence name to add the species abbreviation using the 2 first letters of the name of the transcriptome file : note that each species abbreviation must be unique
2) Selects one allelic sequence from each transcript (c or locus) using the length of the sequence and its level of confidence
3) Selects the best ORF from the sequence between two stop codons
4) Performs a CAP3 from the full set of ORFs to minimize redundancy
5) Retrieves the initial transcript sequences from the remaining set of proceeded ORF sequences
1) Performs a CAP3 from the full set of ORFs to minimize redundancy
2) Merges singlets and contigs identified by CAP3
3) Reformats headers of the FASTA records by adding a specified prefix (defined from the original filename) and ensures that sequences are on a single line
**Outputs**
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Changelog
---------
**Version 2.2 - 07/10/2024**
- Input files can be from any assembly tools
**Version 2.1 - 15/01/2018**
- Input files can be a mix from files coming either from Trinity or Velvet Oases assemblers
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