Tools_Pitagora-Galaxy-0.2.1
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Tool Shed URLRepositoryOwnerRevision
Panel Section
Repo Dep
Tool Dep
Tool
Version
Tool + VersionUsingCommand
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https://testtoolshed.g2.bx.psu.edu/
download_refpitagora329bc367e387Pitagora ToolsNoNoDownload References0.0.1Download References 0.0.1
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://testtoolshed.g2.bx.psu.edu/ -n download_ref -o pitagora -r 329bc367e387 --panel-section-name "Pitagora Tools" --repository-deps --tool-deps
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https://testtoolshed.g2.bx.psu.edu/
filebrowserpitagorad2eb5a5a26a3Pitagora ToolsNoNoLocal File1.0.0Local File 1.0.0
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://testtoolshed.g2.bx.psu.edu/ -n filebrowser -o pitagora -r d2eb5a5a26a3 --panel-section-name "Pitagora Tools" --repository-deps --tool-deps
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https://testtoolshed.g2.bx.psu.edu/
imp_exppitagora4c225e57d44bPitagora ToolsNoNoExport1.0.0Export 1.0.0
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://testtoolshed.g2.bx.psu.edu/ -n imp_exp -o pitagora -r 4c225e57d44b --panel-section-name "Pitagora Tools" --repository-deps --tool-deps
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https://testtoolshed.g2.bx.psu.edu/
imp_exppitagora4c225e57d44bPitagora ToolsNoNoImport1.0.0Import 1.0.0
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://testtoolshed.g2.bx.psu.edu/ -n imp_exp -o pitagora -r 4c225e57d44b --panel-section-name "Pitagora Tools" --repository-deps --tool-deps
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https://testtoolshed.g2.bx.psu.edu/
unix_toolspitagora8fd5091a4091Pitagora ToolsNoNosed1.0.0sed 1.0.0using
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://testtoolshed.g2.bx.psu.edu/ -n unix_tools -o pitagora -r 8fd5091a4091 --panel-section-name "Pitagora Tools" --repository-deps --tool-deps
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https://testtoolshed.g2.bx.psu.edu/
unix_toolspitagora8fd5091a4091Pitagora ToolsNoNoawk0.0.1awk 0.0.1using
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://testtoolshed.g2.bx.psu.edu/ -n unix_tools -o pitagora -r 8fd5091a4091 --panel-section-name "Pitagora Tools" --repository-deps --tool-deps
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https://toolshed.g2.bx.psu.edu/bam_to_sam
devteam
250151b4d934NGS ToolsYesYesBAM-to-SAM1.0.4BAM-to-SAM 1.0.4
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n bam_to_sam -o devteam -r 250151b4d934 --panel-section-name "NGS Tools" --repository-deps --tool-deps
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https://toolshed.g2.bx.psu.edu/bowtie2
devteam
ceb6467e276cNGS ToolsYesYesBowtie20.4Bowtie2 0.4
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n bowtie2 -o devteam -r ceb6467e276c --panel-section-name "NGS Tools" --repository-deps --tool-deps
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https://toolshed.g2.bx.psu.edu/bwa_wrappers
devteam
b4427dbb6cedNGS ToolsYesYes
Map with BWA for Illumina
1.2.3
Map with BWA for Illumina 1.2.3
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n bwa_wrappers -o devteam -r b4427dbb6ced --panel-section-name "NGS Tools" --repository-deps --tool-deps
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https://toolshed.g2.bx.psu.edu/bwa_wrappers
devteam
b4427dbb6cedNGS ToolsYesYesMap with BWA for SOLiD1.0.2Map with BWA for SOLiD 1.0.2
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n bwa_wrappers -o devteam -r b4427dbb6ced --panel-section-name "NGS Tools" --repository-deps --tool-deps
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https://toolshed.g2.bx.psu.edu/cuffdiff
devteam
604fa75232a2RNA-seqYesYesCuffdiff0.0.7Cuffdiff 0.0.7using
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n cuffdiff -o devteam -r 604fa75232a2 --panel-section-name "RNA-seq" --repository-deps --tool-deps
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https://toolshed.g2.bx.psu.edu/cufflinks
devteam
5346d5eea8b1RNA-seqYesYesCufflinks2.2.1.0Cufflinks 2.2.1.0using
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n cufflinks -o devteam -r 5346d5eea8b1 --panel-section-name "RNA-seq" --repository-deps --tool-deps
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https://toolshed.g2.bx.psu.edu/cuffmerge
devteam
b6e3849293b1RNA-seqYesYesCuffmerge2.2.1.0Cuffmerge 2.2.1.0using
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n cuffmerge -o devteam -r b6e3849293b1 --panel-section-name "RNA-seq" --repository-deps --tool-deps
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https://toolshed.g2.bx.psu.edu/elapsed_time
devteam
54da0bd509b0Pitagora ToolsYesYesElapsed time1.0Elapsed time 1.0
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n elapsed_time -o devteam -r 54da0bd509b0 --panel-section-name "Pitagora Tools" --repository-deps --tool-deps
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https://toolshed.g2.bx.psu.edu/fastqc
devteam
0b201de108b9NGS ToolsYesYesFastQC0.63FastQC 0.63using
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n fastqc -o devteam -r 0b201de108b9 --panel-section-name "NGS Tools" --repository-deps --tool-deps
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https://toolshed.g2.bx.psu.edu/join
devteam
de21bdbb8d28GeneralYesYesJoin1.0.0Join 1.0.0using
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n join -o devteam -r de21bdbb8d28 --panel-section-name "General" --repository-deps --tool-deps
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https://toolshed.g2.bx.psu.edu/macs
devteam
ae2ec275332aChIP-seqYesYesMACS1.0.1MACS 1.0.1using
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n macs -o devteam -r ae2ec275332a --panel-section-name "ChIP-seq" --repository-deps --tool-deps
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https://toolshed.g2.bx.psu.edu/macs14ryo-tasc23082638ba0ChIP-seqYesYesMACS141.4.2MACS14 1.4.2
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n macs14 -o ryo-tas -r c23082638ba0 --panel-section-name "ChIP-seq" --repository-deps --tool-deps
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https://toolshed.g2.bx.psu.edu/sam_to_bam
devteam
8176b2575aa1NGS ToolsYesYesSAM-to-BAM1.1.4SAM-to-BAM 1.1.4
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n sam_to_bam -o devteam -r 8176b2575aa1 --panel-section-name "NGS Tools" --repository-deps --tool-deps
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https://toolshed.g2.bx.psu.edu/sql_toolssem4j51847f1c0acbSQL ToolsNoNoSQL0.4SQL 0.4
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n sql_tools -o sem4j -r 51847f1c0acb --panel-section-name "SQL Tools" --repository-deps --tool-deps
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https://toolshed.g2.bx.psu.edu/sql_toolssem4j51847f1c0acbSQL ToolsNoNoTabular to CSV0.2Tabular to CSV 0.2
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n sql_tools -o sem4j -r 51847f1c0acb --panel-section-name "SQL Tools" --repository-deps --tool-deps
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https://toolshed.g2.bx.psu.edu/sql_toolssem4j51847f1c0acbSQL ToolsNoNoEdit Header0.2Edit Header 0.2
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n sql_tools -o sem4j -r 51847f1c0acb --panel-section-name "SQL Tools" --repository-deps --tool-deps
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https://toolshed.g2.bx.psu.edu/tophat2
devteam
da1f39fe14bcRNA-seqYesYesTophat20.7Tophat2 0.7using
python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 1be113aebd32fb048de8d3cc14ad91c3 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n tophat2 -o devteam -r da1f39fe14bc --panel-section-name "RNA-seq" --repository-deps --tool-deps
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(pre-installed)------Join two Datasets2.0.2Join two Datasets 2.0.2
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(pre-installed)------Count1.0.0Count 1.0.0
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(pre-installed)------Cut1.0.2Cut 1.0.2
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