2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5e6311bd7f79/ changeset: r5189:5e6311bd7f79 user: guru date: 2011-03-07 19:30:37 summary: Updated tool help for microsatellite birth/death tools. affected #: 2 files (302 bytes) --- a/tools/regVariation/microsatellite_birthdeath.xml Mon Mar 07 11:43:51 2011 -0500 +++ b/tools/regVariation/microsatellite_birthdeath.xml Mon Mar 07 13:30:37 2011 -0500 @@ -18,8 +18,8 @@ <param format="txt" name="orthfile" type="data" label="Select raw microsatellite data"/> - <param name="tree_definition" size="20" type="text" label="Tree definition of all species above whether or not selected for microsatellite extraction" - help="For example: ((hg18,panTro2),rheMac2)"/> + <param name="tree_definition" size="200" type="text" value= "((((hg18,panTro2),ponAbe2),rheMac2),calJac1)" label="Tree definition of all species above whether or not selected for microsatellite extraction" + help="For example: ((((hg18,panTro2),ponAbe2),rheMac2),calJac1)"/><param name="separation" size="10" type="integer" value="40" label="Total length of flanking DNA used for sequence-similarity comparisons among species" help="A value of 40 means: 20 bp upstream and 20 bp downstream DNA will be used for similarity comparisons."/> --- a/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml Mon Mar 07 11:43:51 2011 -0500 +++ b/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml Mon Mar 07 13:30:37 2011 -0500 @@ -17,13 +17,13 @@ help="A value of 10 means: Adjacent microsatellites separated by less than 10 base pairs will be excluded from the output."/><param name="thresholds" size="15" type="text" value="9,10,12,12" label="Minimum Threshold for the number of repeats for microsatellites" help="A value of 9,10,12,12 means: All monos having fewer than 9 repeats, dis having fewer than 5 repeats, tris having fewer than 4 repeats, tetras having fewer than 3 repeats will be excluded from the output."/> - <param name="species" type="select" label="Species to extract" display="checkboxes" multiple="true"> - <options> - <filter type="data_meta" ref="input1" key="species" /> - </options> - </param> - <param name="treedefinition" size="20" type="text" label="Tree definition of all species above whether or not selected for microsatellite extraction" - help="For example: ((hg17,panTro1),(mm5,rn3),canFam1)"/> + <param name="species" type="select" label="Select species" display="checkboxes" multiple="true" help="NOTE: Currently users are requested to select one of these three combinations: hg18-panTro2-ponAbe2, hg18-panTro2-ponAbe2-rheMac2 or hg18-panTro2-ponAbe2-rheMac2-calJac1"> + <options> + <filter type="data_meta" ref="input1" key="species" /> + </options> + </param> + <param name="treedefinition" size="200" type="text" value = "((((hg18,panTro2),ponAbe2),rheMac2),calJac1)" label="Tree definition of all species above whether or not selected for microsatellite extraction" + help="For example: ((((hg18,panTro2),ponAbe2),rheMac2),calJac1)"/></page></inputs><outputs> http://bitbucket.org/galaxy/galaxy-central/changeset/3819448f02a3/ changeset: r5190:3819448f02a3 user: guru date: 2011-03-07 19:47:16 summary: merge affected #: 0 files (0 bytes) --- a/tools/regVariation/microsatellite_birthdeath.xml Mon Mar 07 13:30:29 2011 -0500 +++ b/tools/regVariation/microsatellite_birthdeath.xml Mon Mar 07 13:47:16 2011 -0500 @@ -18,8 +18,8 @@ <param format="txt" name="orthfile" type="data" label="Select raw microsatellite data"/> - <param name="tree_definition" size="20" type="text" label="Tree definition of all species above whether or not selected for microsatellite extraction" - help="For example: ((hg18,panTro2),rheMac2)"/> + <param name="tree_definition" size="200" type="text" value= "((((hg18,panTro2),ponAbe2),rheMac2),calJac1)" label="Tree definition of all species above whether or not selected for microsatellite extraction" + help="For example: ((((hg18,panTro2),ponAbe2),rheMac2),calJac1)"/><param name="separation" size="10" type="integer" value="40" label="Total length of flanking DNA used for sequence-similarity comparisons among species" help="A value of 40 means: 20 bp upstream and 20 bp downstream DNA will be used for similarity comparisons."/> --- a/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml Mon Mar 07 13:30:29 2011 -0500 +++ b/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml Mon Mar 07 13:47:16 2011 -0500 @@ -17,13 +17,13 @@ help="A value of 10 means: Adjacent microsatellites separated by less than 10 base pairs will be excluded from the output."/><param name="thresholds" size="15" type="text" value="9,10,12,12" label="Minimum Threshold for the number of repeats for microsatellites" help="A value of 9,10,12,12 means: All monos having fewer than 9 repeats, dis having fewer than 5 repeats, tris having fewer than 4 repeats, tetras having fewer than 3 repeats will be excluded from the output."/> - <param name="species" type="select" label="Species to extract" display="checkboxes" multiple="true"> - <options> - <filter type="data_meta" ref="input1" key="species" /> - </options> - </param> - <param name="treedefinition" size="20" type="text" label="Tree definition of all species above whether or not selected for microsatellite extraction" - help="For example: ((hg17,panTro1),(mm5,rn3),canFam1)"/> + <param name="species" type="select" label="Select species" display="checkboxes" multiple="true" help="NOTE: Currently users are requested to select one of these three combinations: hg18-panTro2-ponAbe2, hg18-panTro2-ponAbe2-rheMac2 or hg18-panTro2-ponAbe2-rheMac2-calJac1"> + <options> + <filter type="data_meta" ref="input1" key="species" /> + </options> + </param> + <param name="treedefinition" size="200" type="text" value = "((((hg18,panTro2),ponAbe2),rheMac2),calJac1)" label="Tree definition of all species above whether or not selected for microsatellite extraction" + help="For example: ((((hg18,panTro2),ponAbe2),rheMac2),calJac1)"/></page></inputs><outputs> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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