1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/7b1bc03240c8/ changeset: 7b1bc03240c8 user: richard_burhans date: 2011-06-15 23:10:51 summary: tweaks to get genome diversity tools to pass their functional tests affected #: 4 files (9 bytes)

--- a/tools/genome_diversity/extract_flanking_dna.xml Wed Jun 15 15:51:05 2011 -0400 +++ b/tools/genome_diversity/extract_flanking_dna.xml Wed Jun 15 17:10:51 2011 -0400 @@ -3,7 +3,7 @@

<command interpreter="python2.5"> extract_flanking_dna.py "--input=$input" "--output=$output" "--snps_loc=${GALAXY_DATA_INDEX_DIR}/gd.snps.loc" - #if $override_metadata.value == "0": + #if $override_metadata.choice == "0": "--scaffold_col=${input.metadata.scaffold}" "--pos_col=${input.metadata.pos}" "--species=${input.metadata.species}" #else "--scaffold_col=$scaf_col" "--pos_col=$pos_col" "--species=$species" @@ -18,7 +18,7 @@ <option value="primer3">Primer3 input</option></param><conditional name="override_metadata"> - <param name="value" type="select" format="integer" label="choose columns"> + <param name="choice" type="select" format="integer" label="choose columns"><option value="0" selected="true">No, get columns from metadata</option><option value="1" >Yes, choose columns</option></param> @@ -44,10 +44,10 @@

<tests><test> - <param name="input" value="gd.sample.wsf"/> + <param name="input" value="gd.sample.wsf" ftype="wsf"/><param name="output_format" value="primer3"/> - <param name="override_metadata" value="0"/> - <output name="output" value="gd.extract_flanking_dna.txt"/> + <param name="choice" value="0"/> + <output name="output" file="gd.extract_flanking_dna.txt"/></test></tests>

--- a/tools/genome_diversity/extract_primers.xml Wed Jun 15 15:51:05 2011 -0400 +++ b/tools/genome_diversity/extract_primers.xml Wed Jun 15 17:10:51 2011 -0400 @@ -3,7 +3,7 @@

<command interpreter="python2.5"> extract_primers.py "--input=$input" "--output=$output" "--primers_loc=${GALAXY_DATA_INDEX_DIR}/gd.primers.loc" - #if $override_metadata.value == "0": + #if $override_metadata.choice == "0": "--scaffold_col=${input.metadata.scaffold}" "--pos_col=${input.metadata.pos}" "--species=${input.metadata.species}" #else "--scaffold_col=$scaf_col" "--pos_col=$pos_col" "--species=$species" @@ -13,7 +13,7 @@ <inputs><param format="tabular" name="input" type="data" label="Selected SNPS dataset"/><conditional name="override_metadata"> - <param name="value" type="select" format="integer" label="choose columns"> + <param name="choice" type="select" format="integer" label="choose columns"><option value="0" selected="true">No, get columns from metadata</option><option value="1" >Yes, choose columns</option></param> @@ -39,9 +39,9 @@

<tests><test> - <param name="input" value="gd.sample.wsf"/> - <param name="override_metadata" value="0"/> - <output name="output" value="gd.extract_primers.txt"/> + <param name="input" value="gd.sample.wsf" ftype="wsf"/> + <param name="choice" value="0"/> + <output name="output" file="gd.extract_primers.txt"/></test></tests>

--- a/tools/genome_diversity/select_restriction_enzymes.xml Wed Jun 15 15:51:05 2011 -0400 +++ b/tools/genome_diversity/select_restriction_enzymes.xml Wed Jun 15 17:10:51 2011 -0400 @@ -3,7 +3,7 @@

<command interpreter="python2.5"> select_restriction_enzymes.py "--input=$input" "--output=$output" "--primers_loc=${GALAXY_DATA_INDEX_DIR}/gd.primers.loc" - #if $override_metadata.value == "0": + #if $override_metadata.choice == "0": "--scaffold_col=${input.metadata.scaffold}" "--pos_col=${input.metadata.pos}" "--species=${input.metadata.species}" #else "--scaffold_col=$scaf_col" "--pos_col=$pos_col" "--species=$species" @@ -14,7 +14,7 @@ <inputs><param format="tabular" name="input" type="data" label="Selected SNPS dataset"/><conditional name="override_metadata"> - <param name="value" type="select" format="integer" label="choose columns"> + <param name="choice" type="select" format="integer" label="choose columns"><option value="0" selected="true">No, get columns from metadata</option><option value="1" >Yes, choose columns</option></param> @@ -47,10 +47,10 @@

<tests><test> - <param name="input" value="gd.sample.wsf"/> - <param name="override_metadata" value="0"/> + <param name="input" value="gd.sample.wsf" ftype="wsf"/> + <param name="choice" value="0"/><param name="enzymes" value="BanI,BstOI,Hsp92II"/> - <output name="output" value="gd.select_restrictionenzymes.wsf"/> + <output name="output" file="gd.select_restriction_enzymes.wsf"/></test></tests>

--- a/tools/genome_diversity/select_snps.xml Wed Jun 15 15:51:05 2011 -0400 +++ b/tools/genome_diversity/select_snps.xml Wed Jun 15 17:10:51 2011 -0400 @@ -3,7 +3,7 @@

<command interpreter="python"> select_snps.py "--input=$input" "--output=$output" "--chrlens_loc=${GALAXY_DATA_INDEX_DIR}/gd.chrlens.loc" "--num_snps=$num_snps" - #if $override_metadata.value == "0": + #if $override_metadata.choice == "0": "--ref_chrom_col=${input.metadata.ref}" "--ref_pos_col=${input.metadata.rPos}" "--species=${input.metadata.species}" #else "--ref_chrom_col=$ref_col" "--ref_pos_col=$rpos_col" "--species=$species" @@ -14,7 +14,7 @@ <param format="tabular" name="input" type="data" label="Selected SNPS dataset"/><param name="num_snps" type="integer" value="10" optional="false" min="1" label="Number of SNPs"/><conditional name="override_metadata"> - <param name="value" type="select" format="integer" label="choose columns"> + <param name="choice" type="select" format="integer" label="choose columns"><option value="0" selected="true">No, get columns from metadata</option><option value="1" >Yes, choose columns</option></param> @@ -40,10 +40,10 @@

<tests><test> - <param name="input" value="gd.sample.wsf"/> - <param name="num_snps" value="9"/> - <param name="override_metadata" value="0"/> - <output name="output" value="gd.select_snps.wsf"/> + <param name="input" value="gd.sample.wsf" ftype="wsf"/> + <param name="num_snps" value="5"/> + <param name="choice" value="0"/> + <output name="output" file="gd.select_snps.wsf"/></test></tests>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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