Mercurial > repos > miller-lab > genome_diversity
changeset 4:7a94f11fe71f
change output.extra_files_path to output.files_path
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Tue, 10 Apr 2012 11:58:44 -0400 |
| parents | f810c756a5d6 |
| children | 8a1147101f85 |
| files | coverage_distributions.xml dpmix.xml find_intervals.xml pca.xml phylogenetic_tree.xml population_structure.xml |
| diffstat | 6 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/coverage_distributions.xml Mon Apr 09 16:51:28 2012 -0400 +++ b/coverage_distributions.xml Tue Apr 10 11:58:44 2012 -0400 @@ -2,7 +2,7 @@ <description>distributions</description> <command interpreter="python"> - coverage_distributions.py "$input" "0" "$output" "$output.extra_files_path" + coverage_distributions.py "$input" "0" "$output" "$output.files_path" #if $individuals.choice == '0' "all_individuals" #else if $individuals.choice == '1'
--- a/dpmix.xml Mon Apr 09 16:51:28 2012 -0400 +++ b/dpmix.xml Tue Apr 10 11:58:44 2012 -0400 @@ -2,7 +2,7 @@ <description>using dynamic programming</description> <command interpreter="python"> - dpmix.py "$input" "$data_source" "$switch_penalty" "$ap1_input" "$ap2_input" "$p_input" "$output" "$output2" "$output2.extra_files_path" "$input.dataset.metadata.dbkey" "$input.dataset.metadata.ref" "$GALAXY_DATA_INDEX_DIR" "gd.heterochromatic.loc" + dpmix.py "$input" "$data_source" "$switch_penalty" "$ap1_input" "$ap2_input" "$p_input" "$output" "$output2" "$output2.files_path" "$input.dataset.metadata.dbkey" "$input.dataset.metadata.ref" "$GALAXY_DATA_INDEX_DIR" "gd.heterochromatic.loc" #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) #set $arg = '%s:%s' % ($individual_col, $individual) "$arg"
--- a/find_intervals.xml Mon Apr 09 16:51:28 2012 -0400 +++ b/find_intervals.xml Tue Apr 10 11:58:44 2012 -0400 @@ -2,7 +2,7 @@ <description>genomic intervals</description> <command interpreter="python"> - find_intervals.py "$input" "$input.metadata.dbkey" "$output" "$output.extra_files_path" + find_intervals.py "$input" "$input.metadata.dbkey" "$output" "$output.files_path" #if $override_metadata.choice == "0" "$input.metadata.ref" "$input.metadata.rPos"
--- a/pca.xml Mon Apr 09 16:51:28 2012 -0400 +++ b/pca.xml Tue Apr 10 11:58:44 2012 -0400 @@ -1,7 +1,7 @@ <tool id="gd_pca" name="PCA" version="1.0.0"> <command interpreter="python"> - pca.py "$input" "$input.extra_files_path" "$output" "$output.extra_files_path" + pca.py "$input" "$input.extra_files_path" "$output" "$output.files_path" </command> <inputs>
--- a/phylogenetic_tree.xml Mon Apr 09 16:51:28 2012 -0400 +++ b/phylogenetic_tree.xml Tue Apr 10 11:58:44 2012 -0400 @@ -8,7 +8,7 @@ #else if $individuals.choice == '1' "$p1_input" #end if - "$output" "$output.extra_files_path" "$minimum_coverage" "$minimum_quality" + "$output" "$output.files_path" "$minimum_coverage" "$minimum_quality" #if ((str($input.metadata.scaffold) == str($input.metadata.ref)) and (str($input.metadata.pos) == str($input.metadata.rPos))) or (str($include_reference) == '0') "none" #else
--- a/population_structure.xml Mon Apr 09 16:51:28 2012 -0400 +++ b/population_structure.xml Tue Apr 10 11:58:44 2012 -0400 @@ -2,7 +2,7 @@ <description>structure</description> <command interpreter="python"> - population_structure.py "$input" "${input.extra_files_path}/admix.ped" "$output" "$output.extra_files_path" "$populations" + population_structure.py "$input" "${input.extra_files_path}/admix.ped" "$output" "$output.files_path" "$populations" </command> <inputs>