2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/06b31a61793c/ changeset: 06b31a61793c branch: add_requirement_tags_for_plink user: jmchilton date: 2012-02-06 22:43:05 summary: Adding plink requirement tag for various rgenetics tools requiring plink. affected #: 6 files diff -r 74b6319b38b4b3876d0b81ef1296bb5afc729cc1 -r 06b31a61793c6e3b8ab39676ded73f6af95212f7 tools/rgenetics/rgCaCo.xml --- a/tools/rgenetics/rgCaCo.xml +++ b/tools/rgenetics/rgCaCo.xml @@ -1,4 +1,5 @@ <tool id="rgCaCo1" name="Case Control:"> + <requirements><requirement type="package">plink</requirement></requirements><description>for unrelated subjects</description><command interpreter="python"> rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$title" '$out_file1' '$logf' '$logf.files_path' '$gffout' diff -r 74b6319b38b4b3876d0b81ef1296bb5afc729cc1 -r 06b31a61793c6e3b8ab39676ded73f6af95212f7 tools/rgenetics/rgClean.xml --- a/tools/rgenetics/rgClean.xml +++ b/tools/rgenetics/rgClean.xml @@ -1,4 +1,5 @@ <tool id="rgClean1" name="Clean genotypes:"> + <requirements><requirement type="package">plink</requirement></requirements><description>filter markers, subjects</description><command interpreter="python"> diff -r 74b6319b38b4b3876d0b81ef1296bb5afc729cc1 -r 06b31a61793c6e3b8ab39676ded73f6af95212f7 tools/rgenetics/rgGLM.xml --- a/tools/rgenetics/rgGLM.xml +++ b/tools/rgenetics/rgGLM.xml @@ -1,4 +1,5 @@ <tool id="rgGLM1" name="Linear Models:" version="0.2"> + <requirements><requirement type="package">plink</requirement></requirements><description>for genotype data</description><code file="rgGLM_code.py"/><command interpreter="python"> diff -r 74b6319b38b4b3876d0b81ef1296bb5afc729cc1 -r 06b31a61793c6e3b8ab39676ded73f6af95212f7 tools/rgenetics/rgLDIndep.xml --- a/tools/rgenetics/rgLDIndep.xml +++ b/tools/rgenetics/rgLDIndep.xml @@ -1,4 +1,5 @@ <tool id="rgLDIndep1" name="LD Independent:"> + <requirements><requirement type="package">plink</requirement></requirements><code file="rgLDIndep_code.py"/><description>filter high LD pairs - decrease redundancy</description> diff -r 74b6319b38b4b3876d0b81ef1296bb5afc729cc1 -r 06b31a61793c6e3b8ab39676ded73f6af95212f7 tools/rgenetics/rgQC.xml --- a/tools/rgenetics/rgQC.xml +++ b/tools/rgenetics/rgQC.xml @@ -1,5 +1,6 @@ <tool id="rgQC1" name="QC reports:"> - + <requirements><requirement type="package">plink</requirement></requirements> + <description>Marker and Subject measures</description><command interpreter="python"> diff -r 74b6319b38b4b3876d0b81ef1296bb5afc729cc1 -r 06b31a61793c6e3b8ab39676ded73f6af95212f7 tools/rgenetics/rgTDT.xml --- a/tools/rgenetics/rgTDT.xml +++ b/tools/rgenetics/rgTDT.xml @@ -1,4 +1,6 @@ <tool id="rgTDT1" name="Transmission Distortion:"> + <requirements><requirement type="package">plink</requirement></requirements> + <description>for family data</description><command interpreter="python"> https://bitbucket.org/galaxy/galaxy-central/changeset/4b0d6a9ecef8/ changeset: 4b0d6a9ecef8 user: natefoo date: 2012-08-10 20:33:59 summary: Merged in jmchilton/umn-galaxy-central/add_requirement_tags_for_plink (pull request #35) affected #: 6 files diff -r 35c524274296c33320190a017bc316b57cb4f759 -r 4b0d6a9ecef858e507df4fa04fd8d8c37d542958 tools/rgenetics/rgCaCo.xml --- a/tools/rgenetics/rgCaCo.xml +++ b/tools/rgenetics/rgCaCo.xml @@ -1,4 +1,5 @@ <tool id="rgCaCo1" name="Case Control:"> + <requirements><requirement type="package">plink</requirement></requirements><description>for unrelated subjects</description><command interpreter="python"> rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$title" '$out_file1' '$logf' '$logf.files_path' '$gffout' diff -r 35c524274296c33320190a017bc316b57cb4f759 -r 4b0d6a9ecef858e507df4fa04fd8d8c37d542958 tools/rgenetics/rgClean.xml --- a/tools/rgenetics/rgClean.xml +++ b/tools/rgenetics/rgClean.xml @@ -1,4 +1,5 @@ <tool id="rgClean1" name="Clean genotypes:"> + <requirements><requirement type="package">plink</requirement></requirements><description>filter markers, subjects</description><command interpreter="python"> diff -r 35c524274296c33320190a017bc316b57cb4f759 -r 4b0d6a9ecef858e507df4fa04fd8d8c37d542958 tools/rgenetics/rgGLM.xml --- a/tools/rgenetics/rgGLM.xml +++ b/tools/rgenetics/rgGLM.xml @@ -1,4 +1,5 @@ <tool id="rgGLM1" name="Linear Models:" version="0.2"> + <requirements><requirement type="package">plink</requirement></requirements><description>for genotype data</description><code file="rgGLM_code.py"/><command interpreter="python"> diff -r 35c524274296c33320190a017bc316b57cb4f759 -r 4b0d6a9ecef858e507df4fa04fd8d8c37d542958 tools/rgenetics/rgLDIndep.xml --- a/tools/rgenetics/rgLDIndep.xml +++ b/tools/rgenetics/rgLDIndep.xml @@ -1,4 +1,5 @@ <tool id="rgLDIndep1" name="LD Independent:"> + <requirements><requirement type="package">plink</requirement></requirements><code file="rgLDIndep_code.py"/><description>filter high LD pairs - decrease redundancy</description> diff -r 35c524274296c33320190a017bc316b57cb4f759 -r 4b0d6a9ecef858e507df4fa04fd8d8c37d542958 tools/rgenetics/rgQC.xml --- a/tools/rgenetics/rgQC.xml +++ b/tools/rgenetics/rgQC.xml @@ -1,5 +1,6 @@ <tool id="rgQC1" name="QC reports:"> - + <requirements><requirement type="package">plink</requirement></requirements> + <description>Marker and Subject measures</description><command interpreter="python"> diff -r 35c524274296c33320190a017bc316b57cb4f759 -r 4b0d6a9ecef858e507df4fa04fd8d8c37d542958 tools/rgenetics/rgTDT.xml --- a/tools/rgenetics/rgTDT.xml +++ b/tools/rgenetics/rgTDT.xml @@ -1,4 +1,6 @@ <tool id="rgTDT1" name="Transmission Distortion:"> + <requirements><requirement type="package">plink</requirement></requirements> + <description>for family data</description><command interpreter="python"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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