Mercurial > repos > trinity_ctat > ctat_metagenomics
changeset 2:e5182440ba17 draft
Trying to fix problems with ctat_star_fusion and ctat_metagenomics.
author | trinity_ctat |
---|---|
date | Fri, 13 Apr 2018 14:57:51 -0400 |
parents | 1c8d5eb15ed1 |
children | 983f4f1c7f73 |
files | ctat_metagenomics.xml |
diffstat | 1 files changed, 2 insertions(+), 38 deletions(-) [+] |
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--- a/ctat_metagenomics.xml Thu Apr 12 10:46:59 2018 -0400 +++ b/ctat_metagenomics.xml Fri Apr 13 14:57:51 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="ctat_metagenomics" name="ctat_metagenomics" version=1.0.0 profile="17.05"> +<tool id="ctat_metagenomics" name="ctat_metagenomics" version="1.0.0" profile="17.05"> <description>Centrifuge - Classifier for metagenomic sequences (RNA-Seq)</description> <requirements> @@ -61,7 +61,7 @@ </conditional> <param name="index" type="select" label="Choose reference genome index :" help="Select genome index"> - <options from_data_table="ctat_centrifuge_indexes"> + <options from_data_table="ctat_centrifuge_indexes" /> </param> </inputs> @@ -89,42 +89,6 @@ <output name="classification_report" file="centrifuge/SRR2219890_1.classification.report.txt" /> <output name="kraken_style_report" file="centrifuge/SRR2219890_1.kraken_style_report.txt" /> </test> - <test> - <!-- The following test uses two files that are left/right paired reads. - --> - <param name="format" value="fastq" /> - <param name="type" value="paired" /> - <param name="left_fq" value="centrifuge/SRR073747_1.fastq" /> - <param name="right_fq" value="centrifuge/SRR073747_2.fastq" /> - <!-- FIX - How are we going to set the index value when we don't know what is in the table? How do we find it for testing? - <param name="index.fields.path" value="/N/dc2/projects/galaxyshared/trinity/dev/Trinity_CTAT/metagenomics/phv" /> - --> - <output name="classification_results" > - <assert_contents> - <has_line_matching expression=".+" /> - <has_line line="readID	seqID	taxID	score	2ndBestScore	hitLength	queryLength	numMatches" /> - </assert_contents> - </output> - <output name="classification_report" file="centrifuge/SRR073747_1_2.classification.report.txt" /> - <output name="kraken_style_report" file="centrifuge/SRR073747_1_2.kraken_style_report.txt" /> - </test> - <test> - <!-- The following test uses an unpaired Trinity fasta file. - --> - <param name="format_type.format" value="fasta" /> - <param name="fasta_file" value="centrifuge/TrinitySRR2219890.fasta" /> - <!-- FIX - How are we going to set the index value when we don't know what is in the table? How do we find it for testing? - <param name="index" value="/N/dc2/projects/galaxyshared/trinity/dev/Trinity_CTAT/metagenomics/phv" /> - --> - <output name="classification_results" > - <assert_contents> - <has_line_matching expression=".+" /> - <has_line line="readID	seqID	taxID	score	2ndBestScore	hitLength	queryLength	numMatches" /> - </assert_contents> - </output> - <output name="classification_report" file="centrifuge/TrinitySRR2219890.classification.report.txt" />> - <output name="kraken_style_report" file="centrifuge/TrinitySRR2219890.kraken_style_report.txt" /> - </test> </tests> <help>