| Previous changeset 7:08be1b2b0bf6 (2013-04-25) Next changeset 9:b2eb4f48122f (2013-04-25) |
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Commit message:
Uploaded v0.0.19 preview 5, nicer output labels on datasets |
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modified:
tools/ncbi_blast_plus/ncbi_blast_plus.txt tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml tools/ncbi_blast_plus/ncbi_makeblastdb.xml tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml |
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| diff -r 08be1b2b0bf6 -r e710b9446493 tools/ncbi_blast_plus/ncbi_blast_plus.txt --- a/tools/ncbi_blast_plus/ncbi_blast_plus.txt Thu Apr 25 09:05:13 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blast_plus.txt Thu Apr 25 09:27:16 2013 -0400 |
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| @@ -94,9 +94,10 @@ v0.0.18 - Defensive quoting of filenames in case of spaces (where possible, BLAST+ handling of some mult-file arguments is problematic). v0.0.19 - Added wrappers for rpsblast and rpstblastn, and new blastdb_d.loc - for the domain databases they use (e.g. CDD). + for the domain databases they use (e.g. CDD, PFAM or SMART). - Correct case of exception regular expression (for error handling fall-back in case the return code is not set properly). + - Clearer naming of output files. Developers |
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| diff -r 08be1b2b0bf6 -r e710b9446493 tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Apr 25 09:05:13 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Apr 25 09:27:16 2013 -0400 |
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| @@ -136,7 +136,7 @@ </conditional> </inputs> <outputs> - <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}"> + <data name="output1" format="tabular" label="${blast_type.value_label} on ${on_string}"> <change_format> <when input="out_format" value="0" format="txt"/> <when input="out_format" value="0 -html" format="html"/> |
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| diff -r 08be1b2b0bf6 -r e710b9446493 tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Thu Apr 25 09:05:13 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Thu Apr 25 09:27:16 2013 -0400 |
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| @@ -141,7 +141,7 @@ </conditional> </inputs> <outputs> - <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}"> + <data name="output1" format="tabular" label="${blast_type.value_label} on ${on_string}"> <change_format> <when input="out_format" value="0" format="txt"/> <when input="out_format" value="0 -html" format="html"/> |
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| diff -r 08be1b2b0bf6 -r e710b9446493 tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Thu Apr 25 09:05:13 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Thu Apr 25 09:27:16 2013 -0400 |
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| @@ -158,7 +158,7 @@ </conditional> </inputs> <outputs> - <data name="output1" format="tabular" label="blastx on ${db_opts.db_opts_selector}"> + <data name="output1" format="tabular" label="blastx on ${on_string}"> <change_format> <when input="out_format" value="0" format="txt"/> <when input="out_format" value="0 -html" format="html"/> |
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| diff -r 08be1b2b0bf6 -r e710b9446493 tools/ncbi_blast_plus/ncbi_makeblastdb.xml --- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Thu Apr 25 09:05:13 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Thu Apr 25 09:27:16 2013 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.3"> +<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.4"> <description>Make BLAST database</description> <requirements> <requirement type="binary">makeblastdb</requirement> @@ -95,7 +95,7 @@ </inputs> <outputs> <!-- If we only accepted one FASTA file, we could use its human name here... --> - <data name="outfile" format="data" label="BLAST database from ${on_string}"> + <data name="outfile" format="data" label="${dbtype.value_label} BLAST database from ${on_string}"> <change_format> <when input="dbtype" value="nucl" format="blastdbn"/> <when input="dbtype" value="prot" format="blastdbp"/> |
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| diff -r 08be1b2b0bf6 -r e710b9446493 tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Thu Apr 25 09:05:13 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Thu Apr 25 09:27:16 2013 -0400 |
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| @@ -113,7 +113,7 @@ </conditional> </inputs> <outputs> - <data name="output1" format="tabular" label="RPS-BLAST on ${db_opts.db_opts_selector}"> + <data name="output1" format="tabular" label="rpsblast on ${on_string}"> <change_format> <when input="out_format" value="0" format="txt"/> <when input="out_format" value="0 -html" format="html"/> |
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| diff -r 08be1b2b0bf6 -r e710b9446493 tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Thu Apr 25 09:05:13 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Thu Apr 25 09:27:16 2013 -0400 |
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| @@ -114,7 +114,7 @@ </conditional> </inputs> <outputs> - <data name="output1" format="tabular" label="RPS-TBLASTN on ${db_opts.db_opts_selector}"> + <data name="output1" format="tabular" label="rpstblastn on ${on_string}"> <change_format> <when input="out_format" value="0" format="txt"/> <when input="out_format" value="0 -html" format="html"/> |
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| diff -r 08be1b2b0bf6 -r e710b9446493 tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Apr 25 09:05:13 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Apr 25 09:27:16 2013 -0400 |
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| @@ -158,7 +158,7 @@ </conditional> </inputs> <outputs> - <data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}"> + <data name="output1" format="tabular" label="tblastn on ${on_string}"> <change_format> <when input="out_format" value="0" format="txt"/> <when input="out_format" value="0 -html" format="html"/> |
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| diff -r 08be1b2b0bf6 -r e710b9446493 tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Thu Apr 25 09:05:13 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Thu Apr 25 09:27:16 2013 -0400 |
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| @@ -178,7 +178,7 @@ </conditional> </inputs> <outputs> - <data name="output1" format="tabular" label="tblastx on ${db_opts.db_opts_selector}"> + <data name="output1" format="tabular" label="tblastx on ${on_string}"> <change_format> <when input="out_format" value="0" format="txt"/> <when input="out_format" value="0 -html" format="html"/> |