funtional_test -list shows weird names
Hi, I'm trying to add some test to fastx-toolkit, I pulled a fresh copy, tries "sh run_functional_tests.sh -list" and got the following output: ... ... =========================================================================================================================================== id name section::FASTA_manipulation-fasta_manipulation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fasta_compute_length Compute sequence length fasta_filter_by_length Filter sequences by length fasta_concatenate0 Concatenate fasta2tab FASTA-to-Tabular tab2fasta Tabular-to-FASTA
FASTA Width
_name= RNA/DNA cshl_fastx_collapser Collapse =========================================================================================================================================== id name section::NGS:_QC_and_manipulation-cshl_library_information - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fastq_gen_conv FASTQ Groomer cshl_fastq_quality_converter Quality format converter cshl_fastx_quality_statistics Compute quality statistics cshl_fastq_quality_boxplot Draw quality score boxplot
Draw nucleotides distribution chart
split_paired_reads Split paired end reads quality_score_distribution Build base quality distribution trim_reads Select high quality segments _name= SOLiD-to-FASTQ _name= Compute quality statistics _name= Draw quality score boxplot =========================================================================================================================================== ... ... Some of the tools (e.g. "FASTA width", or even "SOLiD-to-FASTQ" which isn't my tool) shows invalid 'id'. Is this normal? and how do I run test for these tools? thanks, -gordon
Hi Assaf, I'm not sure about the invalid IDs, but to run functional tests, from hte galaxy root try: sh run_functional_tests.sh -id <tool_id> The tool IDs are valid in each tool config. On Dec 5, 2009, at 8:14 PM, Assaf Gordon wrote:
Hi,
I'm trying to add some test to fastx-toolkit,
I pulled a fresh copy, tries "sh run_functional_tests.sh -list" and got the following output: ... ... ====================================================================== ===================================================================== id name section::FASTA_manipulation-fasta_manipulation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fasta_compute_length Compute sequence length fasta_filter_by_length Filter sequences by length fasta_concatenate0 Concatenate fasta2tab FASTA-to-Tabular tab2fasta Tabular-to-FASTA
FASTA Width
_name= RNA/DNA cshl_fastx_collapser Collapse ====================================================================== ===================================================================== id name section::NGS:_QC_and_manipulation-cshl_library_information - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fastq_gen_conv FASTQ Groomer cshl_fastq_quality_converter Quality format converter cshl_fastx_quality_statistics Compute quality statistics cshl_fastq_quality_boxplot Draw quality score boxplot
Draw nucleotides distribution chart
split_paired_reads Split paired end reads quality_score_distribution Build base quality distribution trim_reads Select high quality segments _name= SOLiD-to-FASTQ _name= Compute quality statistics _name= Draw quality score boxplot ====================================================================== ===================================================================== ... ...
Some of the tools (e.g. "FASTA width", or even "SOLiD-to-FASTQ" which isn't my tool) shows invalid 'id'. Is this normal? and how do I run test for these tools?
thanks, -gordon _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
participants (2)
-
Assaf Gordon -
Greg Von Kuster