[galaxy-commits] commit/galaxy-central: 4 new changesets

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3a156f9e008d/ Changeset: 3a156f9e008d User: nsoranzo Date: 2013-09-18 14:43:59 Summary: Prevent no choice in multiple selections. Affected #: 2 files diff -r 750e687b468a27978d51dfac9d542a0cc113e64b -r 3a156f9e008d3e61a951aa9efba2c982cb826e0a tools/ngs_simulation/ngs_simulation.py --- a/tools/ngs_simulation/ngs_simulation.py +++ b/tools/ngs_simulation/ngs_simulation.py @@ -70,11 +70,11 @@ num_sims = int( options.num_sims ) except TypeError, e: stop_err( 'Make sure the number of simulations is an integer value: %s' % str( e ) ) - if len( options.polymorphism ) > 0: + if options.polymorphism != 'None': polymorphisms = [ float( p ) for p in options.polymorphism.split( ',' ) ] else: stop_err( 'Select at least one polymorphism value to use' ) - if len( options.detection_thresh ) > 0: + if options.detection_thresh != 'None': detection_threshes = [ float( dt ) for dt in options.detection_thresh.split( ',' ) ] else: stop_err( 'Select at least one detection threshold to use' ) diff -r 750e687b468a27978d51dfac9d542a0cc113e64b -r 3a156f9e008d3e61a951aa9efba2c982cb826e0a tools/ngs_simulation/ngs_simulation.xml --- a/tools/ngs_simulation/ngs_simulation.xml +++ b/tools/ngs_simulation/ngs_simulation.xml @@ -72,6 +72,7 @@ <option value="0.8">0.8</option><option value="0.9">0.9</option><option value="1.0">1.0</option> + <validator type="no_options" message="You must select at least one value" /></param><param name="detection_thresh" type="select" multiple="true" label="Detection thresholds"><option value="0.001">0.001</option> @@ -102,6 +103,7 @@ <option value="0.8">0.8</option><option value="0.9">0.9</option><option value="1.0">1.0</option> + <validator type="no_options" message="You must select at least one value" /></param><param name="summary_out" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Include a (text) summary file for all the simulations" /><!-- <param name="sim_results" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output all tabular simulation results" help="Number of polymorphisms times number of detection thresholds"/> https://bitbucket.org/galaxy/galaxy-central/commits/ff4bbde97901/ Changeset: ff4bbde97901 User: nsoranzo Date: 2013-09-18 14:44:42 Summary: Fix reference to 'Fetch taxonomic representation' tool. Affected #: 1 file diff -r 3a156f9e008d3e61a951aa9efba2c982cb826e0a -r ff4bbde97901cc3dd3ab9c36432e2d17a655265a tools/taxonomy/t2ps_wrapper.xml --- a/tools/taxonomy/t2ps_wrapper.xml +++ b/tools/taxonomy/t2ps_wrapper.xml @@ -47,7 +47,7 @@ **What it does** -Given taxonomy representation (produced by *Taxonomy manipulation->Fetch Taxonomic Ranks* tool) this utility produces a graphical representations of phylogenetic tree in PDF format. +Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format. -------- https://bitbucket.org/galaxy/galaxy-central/commits/c61cc2f91c59/ Changeset: c61cc2f91c59 User: nsoranzo Date: 2013-10-04 18:15:22 Summary: Fix for "syntax error near unexpected token `;;'". <command> should not end with a semicolon, otherwise BaseJobRunner.build_command_line() would create a bash command containing ';;' when appending metadata setting commands. Affected #: 1 file diff -r ff4bbde97901cc3dd3ab9c36432e2d17a655265a -r c61cc2f91c59c54e585ef92b77f650774ebdbd55 tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -95,15 +95,15 @@ #end if ## view/sort and output file - | samtools view -Su - | samtools sort -o - - > $output; + | samtools view -Su - | samtools sort -o - - > $output ## rename unaligned sequence files #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r: #set left = str($output_unaligned_reads_l).replace( '.dat', '.1.dat' ) #set right = str($output_unaligned_reads_l).replace( '.dat', '.2.dat' ) - mv $left $output_unaligned_reads_l; - mv $right $output_unaligned_reads_r; + ; mv $left $output_unaligned_reads_l; + mv $right $output_unaligned_reads_r #end if </command> https://bitbucket.org/galaxy/galaxy-central/commits/1c22e43fc21e/ Changeset: 1c22e43fc21e User: jmchilton Date: 2013-10-16 19:49:34 Summary: Merged in nsoranzo/galaxy-central-tools2 (pull request #234) Bug fixes for 3 tools (rebased #222) Affected #: 4 files diff -r e8fbf32ba1ccb4edec436e9ca76a40d6f64917be -r 1c22e43fc21e049da34af60f603f2e19bde912d2 tools/ngs_simulation/ngs_simulation.py --- a/tools/ngs_simulation/ngs_simulation.py +++ b/tools/ngs_simulation/ngs_simulation.py @@ -70,11 +70,11 @@ num_sims = int( options.num_sims ) except TypeError, e: stop_err( 'Make sure the number of simulations is an integer value: %s' % str( e ) ) - if len( options.polymorphism ) > 0: + if options.polymorphism != 'None': polymorphisms = [ float( p ) for p in options.polymorphism.split( ',' ) ] else: stop_err( 'Select at least one polymorphism value to use' ) - if len( options.detection_thresh ) > 0: + if options.detection_thresh != 'None': detection_threshes = [ float( dt ) for dt in options.detection_thresh.split( ',' ) ] else: stop_err( 'Select at least one detection threshold to use' ) diff -r e8fbf32ba1ccb4edec436e9ca76a40d6f64917be -r 1c22e43fc21e049da34af60f603f2e19bde912d2 tools/ngs_simulation/ngs_simulation.xml --- a/tools/ngs_simulation/ngs_simulation.xml +++ b/tools/ngs_simulation/ngs_simulation.xml @@ -72,6 +72,7 @@ <option value="0.8">0.8</option><option value="0.9">0.9</option><option value="1.0">1.0</option> + <validator type="no_options" message="You must select at least one value" /></param><param name="detection_thresh" type="select" multiple="true" label="Detection thresholds"><option value="0.001">0.001</option> @@ -102,6 +103,7 @@ <option value="0.8">0.8</option><option value="0.9">0.9</option><option value="1.0">1.0</option> + <validator type="no_options" message="You must select at least one value" /></param><param name="summary_out" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Include a (text) summary file for all the simulations" /><!-- <param name="sim_results" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output all tabular simulation results" help="Number of polymorphisms times number of detection thresholds"/> diff -r e8fbf32ba1ccb4edec436e9ca76a40d6f64917be -r 1c22e43fc21e049da34af60f603f2e19bde912d2 tools/sr_mapping/bowtie2_wrapper.xml --- a/tools/sr_mapping/bowtie2_wrapper.xml +++ b/tools/sr_mapping/bowtie2_wrapper.xml @@ -95,15 +95,15 @@ #end if ## view/sort and output file - | samtools view -Su - | samtools sort -o - - > $output; + | samtools view -Su - | samtools sort -o - - > $output ## rename unaligned sequence files #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r: #set left = str($output_unaligned_reads_l).replace( '.dat', '.1.dat' ) #set right = str($output_unaligned_reads_l).replace( '.dat', '.2.dat' ) - mv $left $output_unaligned_reads_l; - mv $right $output_unaligned_reads_r; + ; mv $left $output_unaligned_reads_l; + mv $right $output_unaligned_reads_r #end if </command> diff -r e8fbf32ba1ccb4edec436e9ca76a40d6f64917be -r 1c22e43fc21e049da34af60f603f2e19bde912d2 tools/taxonomy/t2ps_wrapper.xml --- a/tools/taxonomy/t2ps_wrapper.xml +++ b/tools/taxonomy/t2ps_wrapper.xml @@ -47,7 +47,7 @@ **What it does** -Given taxonomy representation (produced by *Taxonomy manipulation->Fetch Taxonomic Ranks* tool) this utility produces a graphical representations of phylogenetic tree in PDF format. +Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format. -------- Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.