1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1e6f086d98d2/ changeset: 1e6f086d98d2 user: clements date: 2013-01-15 01:13:54 summary: Replaced "query" with "dataset" in a number of tool definition XML files. I got tired of coming across "query" when doing workshops. affected #: 7 files diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/extract/liftOver_wrapper.xml --- a/tools/extract/liftOver_wrapper.xml +++ b/tools/extract/liftOver_wrapper.xml @@ -39,8 +39,8 @@ <param name="minChainT" type="hidden" value="0" /></when><when value="1"> - <param name="minSizeQ" size="10" type="integer" value="0" label="Minimum matching region size in query" help="Recommended value: set to >= 300 bases for complete transcripts"/> - <param name="minChainQ" size="10" type="integer" value="500" label="Minimum chain size in query"/> + <param name="minSizeQ" size="10" type="integer" value="0" label="Minimum matching region size in dataset" help="Recommended value: set to >= 300 bases for complete transcripts"/> + <param name="minChainQ" size="10" type="integer" value="500" label="Minimum chain size in dataset"/><param name="minChainT" size="10" type="integer" value="500" label="Minimum chain size in target"/></when></conditional> diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/filters/bed2gff.xml --- a/tools/filters/bed2gff.xml +++ b/tools/filters/bed2gff.xml @@ -2,7 +2,7 @@ <description>converter</description><command interpreter="python">bed_to_gff_converter.py $input $out_file1</command><inputs> - <param format="bed" name="input" type="data" label="Convert this query"/> + <param format="bed" name="input" type="data" label="Convert this dataset"/></inputs><outputs><data format="gff" name="out_file1" /> diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/filters/condense_characters.xml --- a/tools/filters/condense_characters.xml +++ b/tools/filters/condense_characters.xml @@ -12,7 +12,7 @@ <option value="U">Underscores</option><option value="P">Pipes</option></param> - <param format="txt" name="input" type="data" label="in this Query"/> + <param format="txt" name="input" type="data" label="in this Dataset"/></inputs><outputs><data format="input" name="out_file1" metadata_source="input" /> diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/filters/convert_characters.xml --- a/tools/filters/convert_characters.xml +++ b/tools/filters/convert_characters.xml @@ -13,7 +13,7 @@ <option value="P">Pipes</option><option value="Co">Colons</option></param> - <param format="txt" name="input" type="data" label="in Query"/> + <param format="txt" name="input" type="data" label="in Dataset"/></inputs><outputs><data format="tabular" name="out_file1" /> diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/filters/gff2bed.xml --- a/tools/filters/gff2bed.xml +++ b/tools/filters/gff2bed.xml @@ -2,7 +2,7 @@ <description>converter</description><command interpreter="python">gff_to_bed_converter.py $input $out_file1</command><inputs> - <param format="gff" name="input" type="data" label="Convert this query"/> + <param format="gff" name="input" type="data" label="Convert this dataset"/></inputs><outputs><data format="bed" name="out_file1" /> diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/filters/sorter.xml --- a/tools/filters/sorter.xml +++ b/tools/filters/sorter.xml @@ -14,7 +14,7 @@ #end for </command><inputs> - <param format="tabular" name="input" type="data" label="Sort Query" /> + <param format="tabular" name="input" type="data" label="Sort Dataset" /><param name="column" label="on column" type="data_column" data_ref="input" accept_default="true"/><param name="style" type="select" label="with flavor"><option value="num">Numerical sort</option> diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/new_operations/get_flanks.xml --- a/tools/new_operations/get_flanks.xml +++ b/tools/new_operations/get_flanks.xml @@ -50,11 +50,11 @@ **Example 1** -- For the following query:: +- For the following dataset:: chr22 1000 7000 NM_174568 0 + -- running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Query positive strand; Blue: Flanks output)**:: +- running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Dataset positive strand; Blue: Flanks output)**:: chr22 500 800 NM_174568 0 + @@ -62,11 +62,11 @@ **Example 2** -- For the following query:: +- For the following dataset:: chr22 1000 7000 NM_028946 0 - -- running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Query negative strand; Magenta: Flanks output)**:: +- running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Dataset negative strand; Magenta: Flanks output)**:: chr22 500 800 NM_028946 0 - @@ -75,4 +75,4 @@ </help> -</tool> \ No newline at end of file +</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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