Mercurial > repos > drosofff > mississippi_gcc
changeset 12:2120acb92e0b draft default tip
Deleted selected files
| author | drosofff |
|---|---|
| date | Tue, 24 Jun 2014 11:56:02 -0400 |
| parents | 5839bf207ee6 |
| children | |
| files | mississippi_gcc/annotation_collector.xml mississippi_gcc/bowtie_indices.loc.sample mississippi_gcc/tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 0 insertions(+), 142 deletions(-) [+] |
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--- a/mississippi_gcc/annotation_collector.xml Tue Jun 24 11:40:49 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -<tool id="annotation_collector" name="Collect Annotation counts" version="0.9.0"> - <description> from matched fasta files</description> - <command interpreter="python"> - annotation_collector.py - $out_file - $input1 $label1 - #for $q in $queries - ${q.input2} ${q.label2} - #end for - $title - </command> - <inputs> - <param name="title" type="text" label="Annotation Title"/> - <param name="input1" type="data" label="fasta file to annotate"/> - <param name="label1" type="text" label="category label"/> - <repeat name="queries" title="Additional fasta file and label"> - <param name="input2" type="data" label="Select" /> - <param name="label2" type="text" label="Label" /> - </repeat> - </inputs> - <outputs> - <data name="out_file" format="tabular" metadata_source="input1" label="Annotations"/> - </outputs> - <help> - -.. class:: warningmark - -**WARNING:** Be careful not to agregate datasets of different kinds (e.g., datasets must be matched fasta files). This tool does not check if the datasets being annotated are in the same format. - ------ - -**What it does** - -Generates Annotation Table from fasta files - - </help> -</tool> \ No newline at end of file
--- a/mississippi_gcc/bowtie_indices.loc.sample Tue Jun 24 11:40:49 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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. -#
--- a/mississippi_gcc/tool_data_table_conf.xml.sample Tue Jun 24 11:40:49 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,68 +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 all fasta files under genome directory --> - <table name="all_fasta" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/all_fasta.loc" /> - </table> - <!-- Locations of indexes in the BFAST mapper format --> - <table name="bfast_indexes" comment_char="#"> - <columns>value, dbkey, formats, name, path</columns> - <file path="tool-data/bfast_indexes.loc" /> - </table> - <!-- Locations of nucleotide (mega)blast databases --> - <table name="blastdb" comment_char="#"> - <columns>value, name, path</columns> - <file path="tool-data/blastdb.loc" /> - </table> - <!-- Locations of protein (mega)blast databases --> - <table name="blastdb_p" comment_char="#"> - <columns>value, name, path</columns> - <file path="tool-data/blastdb_p.loc" /> - </table> - <!-- Locations of indexes in the BWA mapper format --> - <table name="bwa_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/bwa_index.loc" /> - </table> - <!-- Locations of indexes in the BWA color-space mapper format --> - <table name="bwa_indexes_color" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/bwa_index_color.loc" /> - </table> - <!-- Locations of MAF files that have been indexed with bx-python --> - <table name="indexed_maf_files"> - <columns>name, value, dbkey, species</columns> - <file path="tool-data/maf_index.loc" /> - </table> - <!-- Locations of fasta files appropriate for NGS simulation --> - <table name="ngs_sim_fasta" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/ngs_sim_fasta.loc" /> - </table> - <!-- Locations of PerM base index files --> - <table name="perm_base_indexes" comment_char="#"> - <columns>value, name, path</columns> - <file path="tool-data/perm_base_index.loc" /> - </table> - <!-- Locations of PerM color-space index files --> - <table name="perm_color_indexes" comment_char="#"> - <columns>value, name, path</columns> - <file path="tool-data/perm_color_index.loc" /> - </table> - <!-- Location of Picard dict file and other files --> - <table name="picard_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/picard_index.loc" /> - </table> - <!-- Location of SRMA dict file and other files --> - <table name="srma_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/picard_index.loc" /> - </table> - <!-- Location of Mosaik files --> - <table name="mosaik_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/mosaik_index.loc" /> - </table> -</tables>