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changeset 10:425378c6dd7c draft

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Uploaded
author ieguinoa
date Fri, 11 Sep 2020 09:17:36 +0000
parents 604e7fbdcf22
children e8aa4f9af3db
files ena_upload.xml tool-data/instrument_model.loc.sample tool-data/instrument_model.txt.sample tool-data/library_layout.loc tool-data/library_layout.txt.sample tool-data/library_selection.loc.sample tool-data/library_selection.txt.sample tool-data/library_source.loc.sample tool-data/library_source.txt.sample tool-data/library_strategy.loc.sample tool-data/library_strategy.txt.sample tool-data/study_type.loc.sample tool-data/study_type.txt.sample tool_data_table_conf.xml.sample
diffstat 14 files changed, 162 insertions(+), 152 deletions(-) [+]
line wrap: on
line diff
--- a/ena_upload.xml	Thu Sep 10 15:00:56 2020 +0000
+++ b/ena_upload.xml	Fri Sep 11 09:17:36 2020 +0000
@@ -137,7 +137,7 @@
                             <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/>
                             <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/>
                             <param name="study_type" type="select" label="Please select the type of study">
-                                    <options from_file="study_type.txt">
+                                    <options from_data_table="study_type">
                                         <column name="value" index="0"/>
                                     </options>
                             </param>
@@ -151,22 +151,22 @@
                                     <param name="experiment_title" type="text" label="Specify an experiment title" />
                                     <param name="experiment_design" type="text" label="Describe the experiment design" />
                                     <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library">
-                                        <options from_file="library_strategy.txt">
+                                        <options from_data_table="library_strategy">
                                             <column name="value" index="0"/>
                                         </options>
                                     </param>
                                     <param name="library_source" type="select" label="Select library source" help="The library source specifies the type of source material that is being sequenced">
-                                        <options from_file="library_source.txt">
+                                        <options from_data_table="library_source">
                                             <column name="value" index="0"/>
                                         </options>
                                     </param>
                                     <param name="library_selection" type="select" label="Library selection" help="The library selection specifies whether any method was used to select for or against, enrich, or screen the material being sequenced">
-                                        <options from_file="library_selection.txt">
+                                        <options from_data_table="library_selection">
                                             <column name="value" index="0"/>
                                         </options>
                                     </param>
                                     <param name="library_layout" type="select" label="Library layout">
-                                        <options from_file="library_layout.txt">
+                                        <options from_data_table="library_layout">
                                             <column name="value" index="0"/>
                                         </options>
                                     </param>
@@ -185,7 +185,7 @@
                                         <option value="CAPILLARY">Capillary sequencing</option>
                                     </param>
                                     <param name="instrument_model" type="select" label="Instrument model">
-                                        <options from_file="instrument_model.txt">
+                                        <options from_data_table="instrument_model">
                                             <column name="value" index="0"/>
                                         </options>
                                     </param>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/instrument_model.loc.sample	Fri Sep 11 09:17:36 2020 +0000
@@ -0,0 +1,58 @@
+minION
+GridION
+PromethION
+454 GS
+454 GS 20
+454 GS FLX
+454 GS FLX+
+454 GS FLX Titanium
+454 GS Junior
+Illumina Genome Analyzer
+Illumina Genome Analyzer II
+Illumina Genome Analyzer IIx
+Illumina HiSeq 1000
+Illumina HiSeq 1500
+Illumina HiSeq 2000
+Illumina HiSeq 2500
+Illumina HiSeq 3000
+Illumina HiSeq 4000
+Illumina iSeq 100
+Illumina HiScanSQ
+Illumina NextSeq 500
+Illumina NextSeq 550
+Illumina NovaSeq 6000
+Illumina HiSeq X Five
+Illumina HiSeq X Ten
+Illumina MiSeq
+Illumina MiniSeq
+AB SOLiD System
+AB SOLiD System 2.0
+AB SOLiD System 3.0
+AB SOLiD 3 Plus System
+AB SOLiD 4 System
+AB SOLiD 4hq System
+AB SOLiD PI System
+AB 5500 Genetic Analyzer
+AB 5500xl Genetic Analyzer
+AB 5500xl-W Genetic Analysis System
+Ion Torrent PGM
+Ion Torrent Proton
+Ion Torrent S5
+Ion Torrent S5 XL
+Complete Genomics
+PacBio RS
+PacBio RS II
+Sequel
+Sequel II
+AB 3730xL Genetic Analyzer
+AB 3730 Genetic Analyzer
+AB 3500xL Genetic Analyzer
+AB 3500 Genetic Analyzer
+AB 3130xL Genetic Analyzer
+AB 3130 Genetic Analyzer
+AB 310 Genetic Analyzer
+BGISEQ-500
+DNBSEQ-T7
+DNBSEQ-G400
+DNBSEQ-G50
+DNBSEQ-G400 FAST
--- a/tool-data/instrument_model.txt.sample	Thu Sep 10 15:00:56 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-minION
-GridION
-PromethION
-454 GS
-454 GS 20
-454 GS FLX
-454 GS FLX+
-454 GS FLX Titanium
-454 GS Junior
-Illumina Genome Analyzer
-Illumina Genome Analyzer II
-Illumina Genome Analyzer IIx
-Illumina HiSeq 1000
-Illumina HiSeq 1500
-Illumina HiSeq 2000
-Illumina HiSeq 2500
-Illumina HiSeq 3000
-Illumina HiSeq 4000
-Illumina iSeq 100
-Illumina HiScanSQ
-Illumina NextSeq 500
-Illumina NextSeq 550
-Illumina NovaSeq 6000
-Illumina HiSeq X Five
-Illumina HiSeq X Ten
-Illumina MiSeq
-Illumina MiniSeq
-AB SOLiD System
-AB SOLiD System 2.0
-AB SOLiD System 3.0
-AB SOLiD 3 Plus System
-AB SOLiD 4 System
-AB SOLiD 4hq System
-AB SOLiD PI System
-AB 5500 Genetic Analyzer
-AB 5500xl Genetic Analyzer
-AB 5500xl-W Genetic Analysis System
-Ion Torrent PGM
-Ion Torrent Proton
-Ion Torrent S5
-Ion Torrent S5 XL
-Complete Genomics
-PacBio RS
-PacBio RS II
-Sequel
-Sequel II
-AB 3730xL Genetic Analyzer
-AB 3730 Genetic Analyzer
-AB 3500xL Genetic Analyzer
-AB 3500 Genetic Analyzer
-AB 3130xL Genetic Analyzer
-AB 3130 Genetic Analyzer
-AB 310 Genetic Analyzer
-BGISEQ-500
-DNBSEQ-T7
-DNBSEQ-G400
-DNBSEQ-G50
-DNBSEQ-G400 FAST
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/library_layout.loc	Fri Sep 11 09:17:36 2020 +0000
@@ -0,0 +1,2 @@
+SINGLE
+PAIRED
--- a/tool-data/library_layout.txt.sample	Thu Sep 10 15:00:56 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-SINGLE
-PAIRED
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/library_selection.loc.sample	Fri Sep 11 09:17:36 2020 +0000
@@ -0,0 +1,27 @@
+RANDOM
+PCR
+RANDOM PCR
+RT-PCR
+HMPR
+MF
+repeat fractionation
+size fractionation
+MSLL
+cDNA
+ChIP
+MNase
+DNase
+Hybrid Selection
+Reduced Representation
+Restriction Digest
+5-methylcytidine antibody
+MBD2 protein methyl-CpG binding domain
+CAGE
+RACE
+MDA
+padlock probes capture method
+Oligo-dT
+Inverse rRNA selection
+ChIP-Seq
+other
+unspecified
--- a/tool-data/library_selection.txt.sample	Thu Sep 10 15:00:56 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-RANDOM
-PCR
-RANDOM PCR
-RT-PCR
-HMPR
-MF
-repeat fractionation
-size fractionation
-MSLL
-cDNA
-ChIP
-MNase
-DNase
-Hybrid Selection
-Reduced Representation
-Restriction Digest
-5-methylcytidine antibody
-MBD2 protein methyl-CpG binding domain
-CAGE
-RACE
-MDA
-padlock probes capture method
-Oligo-dT
-Inverse rRNA selection
-ChIP-Seq
-other
-unspecified
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/library_source.loc.sample	Fri Sep 11 09:17:36 2020 +0000
@@ -0,0 +1,7 @@
+GENOMIC
+TRANSCRIPTOMIC
+METAGENOMIC
+METATRANSCRIPTOMIC
+SYNTHETIC
+VIRAL RNA
+OTHER
--- a/tool-data/library_source.txt.sample	Thu Sep 10 15:00:56 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-GENOMIC
-TRANSCRIPTOMIC
-METAGENOMIC
-METATRANSCRIPTOMIC
-SYNTHETIC
-VIRAL RNA
-OTHER
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/library_strategy.loc.sample	Fri Sep 11 09:17:36 2020 +0000
@@ -0,0 +1,38 @@
+WGS
+WGA
+WXS
+RNA-Seq
+ssRNA-seq
+miRNA-Seq
+ncRNA-Seq
+FL-cDNA
+EST
+Hi-C
+ATAC-seq
+WCS
+RAD-Seq
+CLONE
+POOLCLONE
+AMPLICON
+CLONEEND
+FINISHING
+ChIP-Seq
+MNase-Seq
+DNase-Hypersensitivity
+Bisulfite-Seq
+CTS
+MRE-Seq
+MeDIP-Seq
+MBD-Seq
+Tn-Seq
+VALIDATION
+FAIRE-seq
+SELEX
+RIP-Seq
+ChIA-PET
+Synthetic-Long-Read
+Targeted-Capture
+Tethered Chromatin Conformation Capture
+ChM-Seq
+GBS
+OTHER
--- a/tool-data/library_strategy.txt.sample	Thu Sep 10 15:00:56 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-WGS
-WGA
-WXS
-RNA-Seq
-ssRNA-seq
-miRNA-Seq
-ncRNA-Seq
-FL-cDNA
-EST
-Hi-C
-ATAC-seq
-WCS
-RAD-Seq
-CLONE
-POOLCLONE
-AMPLICON
-CLONEEND
-FINISHING
-ChIP-Seq
-MNase-Seq
-DNase-Hypersensitivity
-Bisulfite-Seq
-CTS
-MRE-Seq
-MeDIP-Seq
-MBD-Seq
-Tn-Seq
-VALIDATION
-FAIRE-seq
-SELEX
-RIP-Seq
-ChIA-PET
-Synthetic-Long-Read
-Targeted-Capture
-Tethered Chromatin Conformation Capture
-ChM-Seq
-GBS
-OTHER
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/study_type.loc.sample	Fri Sep 11 09:17:36 2020 +0000
@@ -0,0 +1,14 @@
+Whole Genome Sequencing
+Metagenomics
+Transcriptome Analysis
+Resequencing
+Epigenetics
+Synthetic Genomics
+Forensic or Paleo-genomics
+Gene Regulation Study
+Cancer Genomics
+Population Genomics
+RNASeq
+Exome Sequencing
+Pooled Clone Sequencing
+Transcriptome Sequencing
--- a/tool-data/study_type.txt.sample	Thu Sep 10 15:00:56 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,14 +0,0 @@
-Whole Genome Sequencing
-Metagenomics
-Transcriptome Analysis
-Resequencing
-Epigenetics
-Synthetic Genomics
-Forensic or Paleo-genomics
-Gene Regulation Study
-Cancer Genomics
-Population Genomics
-RNASeq
-Exome Sequencing
-Pooled Clone Sequencing
-Transcriptome Sequencing
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Sep 11 09:17:36 2020 +0000
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+    <tables>
+        <table name="study_type" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="tool-data/study_type.loc" /></table>
+        <table name="library_layout" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="tool-data/library_layout.loc" /></table>
+        <table name="library_selection" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="tool-data/library_selection.loc" /></table>
+        <table name="instrument_model" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="tool-data/instrument_model.loc" /></table>
+        <table name="library_source" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="tool-data/library_source.loc" /></table>
+        <table name="library_strategy" comment_char="#" allow_duplicate_entries="False"><columns>value</columns><file path="tool-data/library_strategy.loc" /></table>
+    </tables>
+