| Previous changeset 1:6f1378738798 (2017-08-29) Next changeset 3:4d9682bd3a6b (2017-09-02) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 5cf421cdafd250995172684a9db0ac8acbb350b5 |
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modified:
overlapping_reads.xml |
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removed:
tool-data/bowtie_indices.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
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| diff -r 6f1378738798 -r 320e06bf99b9 overlapping_reads.xml --- a/overlapping_reads.xml Tue Aug 29 20:02:15 2017 -0400 +++ b/overlapping_reads.xml Wed Aug 30 05:40:18 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="overlapping_reads" name="Get overlapping reads" version="0.9.0"> +<tool id="overlapping_reads" name="Get overlapping reads" version="0.9.1"> <description /> <requirements> <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> |
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| diff -r 6f1378738798 -r 320e06bf99b9 tool-data/bowtie_indices.loc.sample --- a/tool-data/bowtie_indices.loc.sample Tue Aug 29 20:02:15 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,37 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of Bowtie indexed sequences data files. You will -#need to create these data files and then create a bowtie_indices.loc -#file similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The bowtie_indices.loc -#file has this format (longer white space characters are TAB characters): -# -#<unique_build_id> <dbkey> <display_name> <file_base_path> -# -#So, for example, if you had hg18 indexed stored in -#/depot/data2/galaxy/bowtie/hg18/, -#then the bowtie_indices.loc entry would look like this: -# -#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 -# -#and your /depot/data2/galaxy/bowtie/hg18/ directory -#would contain hg18.*.ebwt files: -# -#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt -#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt -#...etc... -# -#Your bowtie_indices.loc file should include an entry per line for each -#index set you have stored. The "file" in the path does not actually -#exist, but it is the prefix for the actual index files. For example: -# -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon -#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full -#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 -#...etc... -# -#Note that for backwards compatibility with workflows, the unique ID of -#an entry must be the path that was in the original loc file, because that -#is the value stored in the workflow for that parameter. That is why the -#hg19 entry above looks odd. New genomes can be better-looking. -# |
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| diff -r 6f1378738798 -r 320e06bf99b9 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Tue Aug 29 20:02:15 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,8 +0,0 @@ -<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> -<tables> - <!-- Locations of indexes in the Bowtie mapper format --> - <table name="bowtie_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/bowtie_indices.loc" /> - </table> -</tables> |
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| diff -r 6f1378738798 -r 320e06bf99b9 tool_dependencies.xml --- a/tool_dependencies.xml Tue Aug 29 20:02:15 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,18 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="bowtie" version="1.1.2"> - <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="pysam" version="0.8.3"> - <repository changeset_revision="08db58be052a" name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="numpy" version="1.9"> - <repository changeset_revision="f24fc0b630fc" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="R" version="3.1.2"> - <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="biocbasics" version="2.14"> - <repository changeset_revision="f0ef1a7b157e" name="package_biocbasics_2_14" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |