| Previous changeset 4:4afb12181d1a (2013-04-17) Next changeset 6:e77e30f1deeb (2013-04-25) |
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Commit message:
Uploaded v0.0.19 pre-release attempt 2 This defines a package requirement in each wrapper. |
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modified:
tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml 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_tblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml |
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| diff -r 4afb12181d1a -r d42346e675c4 tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Wed Apr 17 09:47:27 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Wed Apr 17 10:04:28 2013 -0400 |
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| @@ -1,5 +1,10 @@ -<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.4"> +<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.5"> <description>Show BLAST database information from blastdbcmd</description> + <requirements> + <requirement type="binary">blastdbcmd</requirement> + <requirement type="package" version="2.2.26+">blast+</requirement> + </requirements> + <version_command>blastdbcmd -version</version_command> <command> blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out "$info" </command> @@ -40,9 +45,6 @@ <outputs> <data name="info" format="txt" label="${db_opts.database.fields.name} info" /> </outputs> - <requirements> - <requirement type="binary">blastdbcmd</requirement> - </requirements> <help> **What it does** |
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| diff -r 4afb12181d1a -r d42346e675c4 tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Wed Apr 17 09:47:27 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Wed Apr 17 10:04:28 2013 -0400 |
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| @@ -1,5 +1,10 @@ -<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.4"> +<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.5"> <description>Extract sequence(s) from BLAST database</description> + <requirements> + <requirement type="binary">blastdbcmd</requirement> + <requirement type="package" version="2.2.26+">blast+</requirement> + </requirements> + <version_command>blastdbcmd -version</version_command> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces @@ -95,9 +100,6 @@ <outputs> <data name="seq" format="fasta" label="Sequences from ${db_opts.database.fields.name}" /> </outputs> - <requirements> - <requirement type="binary">blastdbcmd</requirement> - </requirements> <help> **What it does** |
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| diff -r 4afb12181d1a -r d42346e675c4 tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Wed Apr 17 09:47:27 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Wed Apr 17 10:04:28 2013 -0400 |
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| @@ -2,6 +2,10 @@ <description>Search nucleotide database with nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> + <requirements> + <requirement type="binary">blastn</requirement> + <requirement type="package" version="2.2.26+">blast+</requirement> + </requirements> <version_command>blastn -version</version_command> <command> ## The command is a Cheetah template which allows some Python based syntax. @@ -144,9 +148,6 @@ </change_format> </data> </outputs> - <requirements> - <requirement type="binary">blastn</requirement> - </requirements> <help> .. class:: warningmark |
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| diff -r 4afb12181d1a -r d42346e675c4 tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Wed Apr 17 09:47:27 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Wed Apr 17 10:04:28 2013 -0400 |
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| @@ -2,6 +2,10 @@ <description>Search protein database with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> + <requirements> + <requirement type="binary">blastp</requirement> + <requirement type="package" version="2.2.26+">blast+</requirement> + </requirements> <version_command>blastp -version</version_command> <command> ## The command is a Cheetah template which allows some Python based syntax. @@ -149,9 +153,6 @@ </change_format> </data> </outputs> - <requirements> - <requirement type="binary">blastp</requirement> - </requirements> <tests> <test> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> |
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| diff -r 4afb12181d1a -r d42346e675c4 tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Wed Apr 17 09:47:27 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Wed Apr 17 10:04:28 2013 -0400 |
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| @@ -2,6 +2,10 @@ <description>Search protein database with translated nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> + <requirements> + <requirement type="binary">blastx</requirement> + <requirement type="package" version="2.2.26+">blast+</requirement> + </requirements> <version_command>blastx -version</version_command> <command> ## The command is a Cheetah template which allows some Python based syntax. @@ -166,9 +170,6 @@ </change_format> </data> </outputs> - <requirements> - <requirement type="binary">blastx</requirement> - </requirements> <tests> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
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| diff -r 4afb12181d1a -r d42346e675c4 tools/ncbi_blast_plus/ncbi_makeblastdb.xml --- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Wed Apr 17 09:47:27 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Wed Apr 17 10:04:28 2013 -0400 |
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| @@ -1,7 +1,11 @@ <tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.3"> -<description>Make BLAST database</description> -<version_command>makeblastdb -version</version_command> -<command> + <description>Make BLAST database</description> + <requirements> + <requirement type="binary">makeblastdb</requirement> + <requirement type="package" version="2.2.26+">blast+</requirement> + </requirements> + <version_command>makeblastdb -version</version_command> + <command> makeblastdb -out "${os.path.join($outfile.extra_files_path,'blastdb')}" $parse_seqids $hash_index @@ -100,6 +104,7 @@ </outputs> <requirements> <requirement type="binary">makeblastdb</requirement> + <requirement type="package" version="2.2.26+">blast+</requirement> </requirements> <help> **What it does** |
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| diff -r 4afb12181d1a -r d42346e675c4 tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Wed Apr 17 09:47:27 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Wed Apr 17 10:04:28 2013 -0400 |
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| @@ -2,6 +2,10 @@ <description>Search protein domain database (PSSMs) with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> + <requirements> + <requirement type="binary">rpsblast</requirement> + <requirement type="package" version="2.2.26+">blast+</requirement> + </requirements> <version_command>rpsblast -version</version_command> <command> ## The command is a Cheetah template which allows some Python based syntax. @@ -121,9 +125,6 @@ </change_format> </data> </outputs> - <requirements> - <requirement type="binary">rpsblast</requirement> - </requirements> <help> .. class:: warningmark |
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| diff -r 4afb12181d1a -r d42346e675c4 tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Wed Apr 17 09:47:27 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Wed Apr 17 10:04:28 2013 -0400 |
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| @@ -2,6 +2,10 @@ <description>Search translated nucleotide database with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> + <requirements> + <requirement type="binary">tblastn</requirement> + <requirement type="package" version="2.2.26+">blast+</requirement> + </requirements> <version_command>tblastn -version</version_command> <command> ## The command is a Cheetah template which allows some Python based syntax. @@ -166,9 +170,6 @@ </change_format> </data> </outputs> - <requirements> - <requirement type="binary">tblastn</requirement> - </requirements> <tests> <test> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> |
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| diff -r 4afb12181d1a -r d42346e675c4 tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Wed Apr 17 09:47:27 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Wed Apr 17 10:04:28 2013 -0400 |
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| @@ -2,6 +2,10 @@ <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> + <requirements> + <requirement type="binary">tblastx</requirement> + <requirement type="package" version="2.2.26+">blast+</requirement> + </requirements> <version_command>tblastx -version</version_command> <command> ## The command is a Cheetah template which allows some Python based syntax. @@ -186,9 +190,6 @@ </change_format> </data> </outputs> - <requirements> - <requirement type="binary">tblastx</requirement> - </requirements> <help> .. class:: warningmark |