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changeset 7:85b520815e85 draft

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Uploaded
author florianbegusch
date Tue, 13 Aug 2019 07:53:59 -0400
parents de4c22a52df4
children d66c7509e8f9
files qiime2/qiime_rep_set.loc qiime2/qiime_taxonomy.loc tool_data/qiime_rep_set.loc tool_data/qiime_taxonomy.loc tool_data/ref_classifier.loc tool_data/ref_taxnonomy.loc tool_data_table_conf.xml.sample
diffstat 7 files changed, 38 insertions(+), 17 deletions(-) [+]
line wrap: on
line diff
--- a/qiime2/qiime_rep_set.loc	Tue Aug 13 07:46:48 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-silva_132_release_rep_set_all_99_silva132_99	silva (132_release) - rep_set_all - 99 - 99_otus	silva_132_release_rep_set_all_99_silva132_99.fna	/home/galaxy/galaxy/tool-data/qiime_rep_set/silva_132_release_rep_set_all_99_silva132_99.fna
-silva_132_release_rep_set_all_97_silva132_97	silva (132_release) - rep_set_all - 97 - 97_otus	silva_132_release_rep_set_all_97_silva132_97.fna	/home/galaxy/galaxy/tool-data/qiime_rep_set/silva_132_release_rep_set_all_97_silva132_97.fna
-silva_128_release_rep_set_all_97_97_otus	silva (128_release) - rep_set_all - 97 - 97_otus	silva_128_release_rep_set_all_97_97_otus.fasta	/home/galaxy/galaxy/tool-data/qiime_rep_set/silva_128_release_rep_set_all_97_97_otus.fasta
-unite_20.11.2016_sh_refs_qiime_ver7_97_20.11.2016	unite (20.11.2016) - sh_refs_qiime_ver7_97_20	unite_20.11.2016_sh_refs_qiime_ver7_97_20.11.2016.fasta	/home/galaxy/galaxy/tool-data/qiime_rep_set/unite_20.11.2016_sh_refs_qiime_ver7_97_20.11.2016.fasta
-greengenes_13_8_97_otus	greengenes (13_8_relese) - 97_otus	greengenes_13_8_97_otus.fasta	/home/galaxy/galaxy/tool-data/qiime_rep_set/greengenes_13_8_97_otus.fasta
-greengenes_13_8_99_otus	greengenes (13_8_relese) - 99_otus	greengenes_13_8_99_otus.fasta	/home/galaxy/galaxy/tool-data/qiime_rep_set/greengenes_13_8_99_otus.fasta
-GreenGenes_13_8_99_V4_GTGCCAGCMGCCGCGGTAA_GGACTACHVHHHTWTCTAAT	GreenGenes_13_8_99_V4_GTGCCAGCMGCCGCGGTAA_GGACTACHVHHHTWTCTAAT	GreenGenes_13_8_99_V4_GTGCCAGCMGCCGCGGTAA_GGACTACHVHHHTWTCTAAT.qza	/home/galaxy/galaxy/tool-data/QIIME2_reference_classifiers/GreenGenes_13_8_99_V4_GTGCCAGCMGCCGCGGTAA_GGACTACHVHHHTWTCTAAT.qza
-GreenGenes_13_8_99_V4_GTGYCAGCMGCCGCGGTAA_GGACTACNVGGGTWTCTAAT	GreenGenes_13_8_99_V4_GTGYCAGCMGCCGCGGTAA_GGACTACNVGGGTWTCTAAT	GreenGenes_13_8_99_V4_GTGYCAGCMGCCGCGGTAA_GGACTACNVGGGTWTCTAAT.qza	/home/galaxy/galaxy/tool-data/QIIME2_reference_classifiers/GreenGenes_13_8_99_V4_GTGYCAGCMGCCGCGGTAA_GGACTACNVGGGTWTCTAAT.qza
-GreenGenes_13_8_97_V1_V2_AGAGTTTGATCCTGGCTCAG_CTGCTGCCTYCCGTA	GreenGenes_13_8_97_V1_V2_AGAGTTTGATCCTGGCTCAG_CTGCTGCCTYCCGTA	GreenGenes_13_8_97_V1_V2_AGAGTTTGATCCTGGCTCAG_CTGCTGCCTYCCGTA.qza	/home/galaxy/galaxy/tool-data/QIIME2_reference_classifiers/GreenGenes_13_8_97_V1_V2_AGAGTTTGATCCTGGCTCAG_CTGCTGCCTYCCGTA.qza
--- a/qiime2/qiime_taxonomy.loc	Tue Aug 13 07:46:48 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-silva_132_release_taxonomy_all_99_taxonomy_all_levels	silva (132_release) - taxonomy_all - 99 - taxonomy_all_levels	silva_132_release_taxonomy_all_99_taxonomy_all_levels.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/silva_132_release_taxonomy_all_99_taxonomy_all_levels.txt	
-silva_132_release_taxonomy_all_97_taxonomy_all_levels	silva (132_release) - taxonomy_all - 97 - taxonomy_all_levels	silva_132_release_taxonomy_all_97_taxonomy_all_levels.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/silva_132_release_taxonomy_all_97_taxonomy_all_levels.txt	
-greengenes_13_8_97_otu_taxonomy	greengenes (13_8) - 97_otu_taxonomy	greengenes_13_8_97_otu_taxonomy.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/greengenes_13_8_97_otu_taxonomy.txt	
-greengenes_13_8_99_otu_taxonomy	greengenes (13_8) - 99_otu_taxonomy	greengenes_13_8_99_otu_taxonomy.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/greengenes_13_8_99_otu_taxonomy.txt	
-silva_128_release_taxonomy_all_97_taxonomy_all_levels	silva (128_release) - taxonomy_all - 97 - taxonomy_all_levels	silva_128_release_taxonomy_all_97_taxonomy_all_levels.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/silva_128_release_taxonomy_all_97_taxonomy_all_levels.txt	
-unite_20.11.2016_sh_taxonomy_qiime_ver7_97_20.11.2016	unite (20.11.2016) - sh_taxonomy_qiime_ver7_97_20	unite_20.11.2016_sh_taxonomy_qiime_ver7_97_20.11.2016.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/unite_20.11.2016_sh_taxonomy_qiime_ver7_97_20.11.2016.txt	
-taxmap_ncbi_ssu_ref_132	taxmap_ncbi_ssu_ref_132	taxmap_ncbi_ssu_ref_132.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/taxmap_ncbi_ssu_ref_132.txt	
-taxmap_slv_ssu_ref_132	taxmap_slv_ssu_ref_132	taxmap_slv_ssu_ref_132.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/taxmap_slv_ssu_ref_132.txt	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data/qiime_rep_set.loc	Tue Aug 13 07:53:59 2019 -0400
@@ -0,0 +1,9 @@
+silva_132_release_rep_set_all_99_silva132_99	silva (132_release) - rep_set_all - 99 - 99_otus	silva_132_release_rep_set_all_99_silva132_99.fna	/home/galaxy/galaxy/tool-data/qiime_rep_set/silva_132_release_rep_set_all_99_silva132_99.fna
+silva_132_release_rep_set_all_97_silva132_97	silva (132_release) - rep_set_all - 97 - 97_otus	silva_132_release_rep_set_all_97_silva132_97.fna	/home/galaxy/galaxy/tool-data/qiime_rep_set/silva_132_release_rep_set_all_97_silva132_97.fna
+silva_128_release_rep_set_all_97_97_otus	silva (128_release) - rep_set_all - 97 - 97_otus	silva_128_release_rep_set_all_97_97_otus.fasta	/home/galaxy/galaxy/tool-data/qiime_rep_set/silva_128_release_rep_set_all_97_97_otus.fasta
+unite_20.11.2016_sh_refs_qiime_ver7_97_20.11.2016	unite (20.11.2016) - sh_refs_qiime_ver7_97_20	unite_20.11.2016_sh_refs_qiime_ver7_97_20.11.2016.fasta	/home/galaxy/galaxy/tool-data/qiime_rep_set/unite_20.11.2016_sh_refs_qiime_ver7_97_20.11.2016.fasta
+greengenes_13_8_97_otus	greengenes (13_8_relese) - 97_otus	greengenes_13_8_97_otus.fasta	/home/galaxy/galaxy/tool-data/qiime_rep_set/greengenes_13_8_97_otus.fasta
+greengenes_13_8_99_otus	greengenes (13_8_relese) - 99_otus	greengenes_13_8_99_otus.fasta	/home/galaxy/galaxy/tool-data/qiime_rep_set/greengenes_13_8_99_otus.fasta
+GreenGenes_13_8_99_V4_GTGCCAGCMGCCGCGGTAA_GGACTACHVHHHTWTCTAAT	GreenGenes_13_8_99_V4_GTGCCAGCMGCCGCGGTAA_GGACTACHVHHHTWTCTAAT	GreenGenes_13_8_99_V4_GTGCCAGCMGCCGCGGTAA_GGACTACHVHHHTWTCTAAT.qza	/home/galaxy/galaxy/tool-data/QIIME2_reference_classifiers/GreenGenes_13_8_99_V4_GTGCCAGCMGCCGCGGTAA_GGACTACHVHHHTWTCTAAT.qza
+GreenGenes_13_8_99_V4_GTGYCAGCMGCCGCGGTAA_GGACTACNVGGGTWTCTAAT	GreenGenes_13_8_99_V4_GTGYCAGCMGCCGCGGTAA_GGACTACNVGGGTWTCTAAT	GreenGenes_13_8_99_V4_GTGYCAGCMGCCGCGGTAA_GGACTACNVGGGTWTCTAAT.qza	/home/galaxy/galaxy/tool-data/QIIME2_reference_classifiers/GreenGenes_13_8_99_V4_GTGYCAGCMGCCGCGGTAA_GGACTACNVGGGTWTCTAAT.qza
+GreenGenes_13_8_97_V1_V2_AGAGTTTGATCCTGGCTCAG_CTGCTGCCTYCCGTA	GreenGenes_13_8_97_V1_V2_AGAGTTTGATCCTGGCTCAG_CTGCTGCCTYCCGTA	GreenGenes_13_8_97_V1_V2_AGAGTTTGATCCTGGCTCAG_CTGCTGCCTYCCGTA.qza	/home/galaxy/galaxy/tool-data/QIIME2_reference_classifiers/GreenGenes_13_8_97_V1_V2_AGAGTTTGATCCTGGCTCAG_CTGCTGCCTYCCGTA.qza
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data/qiime_taxonomy.loc	Tue Aug 13 07:53:59 2019 -0400
@@ -0,0 +1,8 @@
+silva_132_release_taxonomy_all_99_taxonomy_all_levels	silva (132_release) - taxonomy_all - 99 - taxonomy_all_levels	silva_132_release_taxonomy_all_99_taxonomy_all_levels.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/silva_132_release_taxonomy_all_99_taxonomy_all_levels.txt	
+silva_132_release_taxonomy_all_97_taxonomy_all_levels	silva (132_release) - taxonomy_all - 97 - taxonomy_all_levels	silva_132_release_taxonomy_all_97_taxonomy_all_levels.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/silva_132_release_taxonomy_all_97_taxonomy_all_levels.txt	
+greengenes_13_8_97_otu_taxonomy	greengenes (13_8) - 97_otu_taxonomy	greengenes_13_8_97_otu_taxonomy.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/greengenes_13_8_97_otu_taxonomy.txt	
+greengenes_13_8_99_otu_taxonomy	greengenes (13_8) - 99_otu_taxonomy	greengenes_13_8_99_otu_taxonomy.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/greengenes_13_8_99_otu_taxonomy.txt	
+silva_128_release_taxonomy_all_97_taxonomy_all_levels	silva (128_release) - taxonomy_all - 97 - taxonomy_all_levels	silva_128_release_taxonomy_all_97_taxonomy_all_levels.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/silva_128_release_taxonomy_all_97_taxonomy_all_levels.txt	
+unite_20.11.2016_sh_taxonomy_qiime_ver7_97_20.11.2016	unite (20.11.2016) - sh_taxonomy_qiime_ver7_97_20	unite_20.11.2016_sh_taxonomy_qiime_ver7_97_20.11.2016.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/unite_20.11.2016_sh_taxonomy_qiime_ver7_97_20.11.2016.txt	
+taxmap_ncbi_ssu_ref_132	taxmap_ncbi_ssu_ref_132	taxmap_ncbi_ssu_ref_132.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/taxmap_ncbi_ssu_ref_132.txt	
+taxmap_slv_ssu_ref_132	taxmap_slv_ssu_ref_132	taxmap_slv_ssu_ref_132.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/taxmap_slv_ssu_ref_132.txt	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data/ref_classifier.loc	Tue Aug 13 07:53:59 2019 -0400
@@ -0,0 +1,5 @@
+#<unique_id>  <name>  <database_caption>  <qza_file_path>
+#
+#For each reference database, you need to download the qza file in qiime path
+#
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data/ref_taxnonomy.loc	Tue Aug 13 07:53:59 2019 -0400
@@ -0,0 +1,5 @@
+#<unique_id>  <name>  <database_caption>  <qza_file_path>
+#
+#For each reference database, you need to download the qza file in qiime path
+#
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Aug 13 07:53:59 2019 -0400
@@ -0,0 +1,11 @@
+<tables>
+    <table name="taxonomy_fp" comment_char="#">
+        <columns>value, name, dbkey, path</columns>
+        <file path="tool_data/ref_taxnonomy.loc" />
+    </table>
+    <table name="classifier_fp" comment_char="#">
+        <columns>value, name, dbkey, path</columns>
+        <file path="tool-data/ref_classifier.loc" />
+    </table>
+</tables>
+