Previous changeset 18:577d9c12411a (2015-09-07) Next changeset 20:3034ce97dd33 (2016-11-07) |
Commit message:
v0.1.07 - fix macro problem in blastxml_to_tabular.xml, reenable .loc tests |
modified:
tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/blastxml_to_tabular.xml 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_macros.xml tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml tools/ncbi_blast_plus/tool_dependencies.xml |
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diff -r 577d9c12411a -r 7f3c448e119b tools/ncbi_blast_plus/README.rst --- a/tools/ncbi_blast_plus/README.rst Mon Sep 07 04:44:24 2015 -0400 +++ b/tools/ncbi_blast_plus/README.rst Thu Nov 19 06:30:35 2015 -0500 |
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@@ -223,6 +223,10 @@ - Update citation information now GigaScience paper is out. v0.1.06 - Now depends on ``package_blast_plus_2_2_31`` in ToolShed. - Tests updated for BLAST+ 2.2.31 instead of BLAST+ 2.2.30. +v0.1.07 - Re-enabled some ``*.loc`` file tests (these had not been supported + on the Tool Shed test framework, but that is not currently in use). + - Fixed macro problem with version field in blastxml_to_tabular.xml + (contribution from Bjoern Gruening and Daniel Blankenberg). ======= ====================================================================== |
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diff -r 577d9c12411a -r 7f3c448e119b tools/ncbi_blast_plus/blastxml_to_tabular.xml --- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml Mon Sep 07 04:44:24 2015 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Thu Nov 19 06:30:35 2015 -0500 |
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@@ -1,5 +1,8 @@ <tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="@WRAPPER_VERSION@"> <description>Convert BLAST XML output to tabular</description> + <macros> + <import>ncbi_macros.xml</import> + </macros> <stdio> <!-- Anything other than zero is an error --> <exit_code range="1:" /> |
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diff -r 577d9c12411a -r 7f3c448e119b tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Mon Sep 07 04:44:24 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Thu Nov 19 06:30:35 2015 -0500 |
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@@ -15,8 +15,6 @@ <data name="info" format="txt" label="${db_opts.database.fields.name} info" /> </outputs> <tests> - <!-- Disable for ToolShed where *.loc tests not yet supported - See https://github.com/peterjc/galaxy_blast/issues/53 <test> <param name="db_opts|db_type" value="prot" /> <param name="db_opts|database" value="four_human_proteins" /> @@ -27,7 +25,6 @@ <param name="db_opts|database" value="three_human_mRNA" /> <output name="info" file="three_human_mRNA.dbinfo.txt" ftype="txt" lines_diff="4" /> </test> - --> </tests> <help> |
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diff -r 577d9c12411a -r 7f3c448e119b tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Mon Sep 07 04:44:24 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Thu Nov 19 06:30:35 2015 -0500 |
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@@ -70,8 +70,6 @@ <data name="seq" format="fasta" label="Sequences from ${db_opts.database.fields.name}" /> </outputs> <tests> - <!-- Disable for ToolShed where *.loc tests not yet supported - See https://github.com/peterjc/galaxy_blast/issues/53 <test> <param name="db_opts|db_type" value="prot" /> <param name="db_opts|database" value="four_human_proteins" /> @@ -80,7 +78,6 @@ <param name="outfmt" value="original" /> <output name="seq" file="four_human_proteins.fasta" ftype="fasta" /> </test> - --> </tests> <help> |
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diff -r 577d9c12411a -r 7f3c448e119b tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Mon Sep 07 04:44:24 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Nov 19 06:30:35 2015 -0500 |
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@@ -102,8 +102,6 @@ <param name="adv_opts_selector" value="basic" /> <output name="output1" file="blastn_rhodopsin_vs_three_human.columns.tabular" ftype="tabular" /> </test> - <!-- Disable for ToolShed where *.loc tests not yet supported - See https://github.com/peterjc/galaxy_blast/issues/53 <test> <param name="query" value="chimera.fasta" ftype="fasta" /> <param name="db_opts_selector" value="db" /> @@ -122,7 +120,6 @@ <param name="max_hits" value="1" /> <output name="output1" file="blastn_chimera_vs_three_human_max1.txt" ftype="txt" /> </test> - --> </tests> <help> |
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diff -r 577d9c12411a -r 7f3c448e119b tools/ncbi_blast_plus/ncbi_macros.xml --- a/tools/ncbi_blast_plus/ncbi_macros.xml Mon Sep 07 04:44:24 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Thu Nov 19 06:30:35 2015 -0500 |
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@@ -1,5 +1,5 @@ <macros> - <token name="@WRAPPER_VERSION@">0.1.06</token> + <token name="@WRAPPER_VERSION@">0.1.07</token> <xml name="parallelism"> <!-- 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" merge_outputs="output1" /> |
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diff -r 577d9c12411a -r 7f3c448e119b tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Mon Sep 07 04:44:24 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Thu Nov 19 06:30:35 2015 -0500 |
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@@ -51,8 +51,6 @@ </data> </outputs> <tests> - <!-- Disable for ToolShed where *.loc tests not yet supported - See https://github.com/peterjc/galaxy_blast/issues/53 <test> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> <param name="db_opts_selector" value="db" /> @@ -61,7 +59,6 @@ <param name="out_format" value="6" /> <output name="output1" file="empty_file.dat" ftype="tabular" /> </test> - --> </tests> <help> |
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diff -r 577d9c12411a -r 7f3c448e119b tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Mon Sep 07 04:44:24 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Thu Nov 19 06:30:35 2015 -0500 |
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@@ -51,8 +51,6 @@ </data> </outputs> <tests> - <!-- Disable for ToolShed where *.loc tests not yet supported - See https://github.com/peterjc/galaxy_blast/issues/53 <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> <param name="db_opts_selector" value="db" /> @@ -61,7 +59,6 @@ <param name="out_format" value="6" /> <output name="output1" file="empty_file.dat" ftype="tabular" /> </test> - --> </tests> <help> |
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diff -r 577d9c12411a -r 7f3c448e119b tools/ncbi_blast_plus/tool_dependencies.xml --- a/tools/ncbi_blast_plus/tool_dependencies.xml Mon Sep 07 04:44:24 2015 -0400 +++ b/tools/ncbi_blast_plus/tool_dependencies.xml Thu Nov 19 06:30:35 2015 -0500 |
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@@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="blast+" version="2.2.31"> - <repository changeset_revision="e36f75574aec" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="16e1254ed634" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |