Repository 'ebi_metagenomics_run_downloader'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/ebi_metagenomics_run_downloader

Changeset 3:a1ef6c88ee37 (2017-02-09)
Previous changeset 2:6155fa39a899 (2017-01-21)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 31d1c92a4c12b6a78693dc5091a08536a075285e
modified:
ebeye_urllib.py
generate_macros.py
macros.xml
b
diff -r 6155fa39a899 -r a1ef6c88ee37 ebeye_urllib.py
--- a/ebeye_urllib.py Sat Jan 21 14:40:54 2017 -0500
+++ b/ebeye_urllib.py Thu Feb 09 12:02:47 2017 -0500
b
@@ -5,6 +5,9 @@
 # and distributed under the Apache License
 # ======================================================================
 # Load libraries
+
+from __future__ import print_function
+
 import os
 import platform
 import re
@@ -269,7 +272,7 @@
     printDebugMessage('getEntries', 'End', 1)
     p = re.compile('http')
     fieldURL = p.sub('https', fieldURL)
-    print fieldURL
+    print(fieldURL)
 
 
 if __name__ == '__main__':
b
diff -r 6155fa39a899 -r a1ef6c88ee37 generate_macros.py
--- a/generate_macros.py Sat Jan 21 14:40:54 2017 -0500
+++ b/generate_macros.py Thu Feb 09 12:02:47 2017 -0500
b
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python
 
 import ebeye_urllib
 
b
diff -r 6155fa39a899 -r a1ef6c88ee37 macros.xml
--- a/macros.xml Sat Jan 21 14:40:54 2017 -0500
+++ b/macros.xml Thu Feb 09 12:02:47 2017 -0500
b
b'@@ -53,6 +53,7 @@\n                 <option value="imgt-hla">IMGT/HLA</option>\n                 <option value="ipd-kir">IPD-KIR</option>\n                 <option value="ipd-mhc">IPD-MHC</option>\n+                <option value="identifiers_registry">Identifiers.org registry</option>\n                 <option value="intact-complexes">IntAct Complexes</option>\n                 <option value="intact-experiments">IntAct Experiments</option>\n                 <option value="intact-interactions">IntAct Interactions</option>\n@@ -495,7 +496,6 @@\n                 <param name="fields" type="select" multiple="true" optional="false" label="Fields to extract">\n                     <option value="BIOSAMPLE" selected="true">BIOSAMPLE</option>\n                     <option value="DOI" selected="true">DOI</option>\n-                    <option value="EC" selected="true">EC</option>\n                     <option value="EMBLCDS" selected="true">EMBLCDS</option>\n                     <option value="ENA" selected="true">ENA</option>\n                     <option value="ENA-CON" selected="true">ENA-CON</option>\n@@ -524,7 +524,6 @@\n                     <param name="query_field" type="select" label="Fields">\n                         <option value="BIOSAMPLE">BIOSAMPLE</option>\n                         <option value="DOI">DOI</option>\n-                        <option value="EC">EC</option>\n                         <option value="EMBLCDS">EMBLCDS</option>\n                         <option value="EMBLCDS_version">EMBLCDS_version</option>\n                         <option value="ENA">ENA</option>\n@@ -547,7 +546,6 @@\n                         <option value="UNIPROTKB_TREMBL">UNIPROTKB_TREMBL</option>\n                         <option value="WORMBASE">WORMBASE</option>\n                         <option value="acc">acc</option>\n-                        <option value="bio_material">bio_material</option>\n                         <option value="creation_date">creation_date</option>\n                         <option value="culture_collection">culture_collection</option>\n                         <option value="data_class">data_class</option>\n@@ -1751,7 +1749,6 @@\n                         <option value="UNIPROT">UNIPROT</option>\n                         <option value="age">age</option>\n                         <option value="biopsy_site">biopsy_site</option>\n-                        <option value="biotic_plant_treatment">biotic_plant_treatment</option>\n                         <option value="block">block</option>\n                         <option value="cell_cycle_stage">cell_cycle_stage</option>\n                         <option value="cell_line">cell_line</option>\n@@ -3952,6 +3949,73 @@\n                 </repeat>\n             </when>\n \n+            <when value="identifiers_registry">\n+                <param name="fields" type="select" multiple="true" optional="false" label="Fields to extract">\n+                    <option value="COLLECTION" selected="true">COLLECTION</option>\n+                    <option value="PUBMED" selected="true">PUBMED</option>\n+                    <option value="description" selected="true">description</option>\n+                    <option value="domain_source" selected="true">domain_source</option>\n+                    <option value="id" selected="true">id</option>\n+                    <option value="institution" selected="true">institution</option>\n+                    <option value="location" selected="true">location</option>\n+                    <option value="name" selected="true">name</option>\n+                    <option value="obsolete" selected="true">obsolete</option>\n+                    <option value="official" selected="true">official</option>\n+                    <option value="pattern" selected="true">pattern</option>\n+                    <option value="tag" selected="true">tag</option>\n+                    <option value="type" selected="true">type</option>\n+                    <option value="uptime" selected="true">uptime</option>\n+     '..b'>SABIO-RK</option>\n                         <option value="SAM">SAM</option>\n+                        <option value="SFLD">SFLD</option>\n                         <option value="SGD">SGD</option>\n                         <option value="SIGNALINK">SIGNALINK</option>\n                         <option value="SIGNOR">SIGNOR</option>\n@@ -9147,21 +9215,19 @@\n                     <option value="NCBI_TAXONOMY_ID" selected="true">NCBI_TAXONOMY_ID</option>\n                     <option value="PDB" selected="true">PDB</option>\n                     <option value="PROTEIN_ID" selected="true">PROTEIN_ID</option>\n-                    <option value="REACTOME" selected="true">REACTOME</option>\n                     <option value="REFSEQ_MRNA" selected="true">REFSEQ_MRNA</option>\n                     <option value="REFSEQ_MRNA_PREDICTED" selected="true">REFSEQ_MRNA_PREDICTED</option>\n                     <option value="REFSEQ_NCRNA" selected="true">REFSEQ_NCRNA</option>\n                     <option value="REFSEQ_PEPTIDE" selected="true">REFSEQ_PEPTIDE</option>\n                     <option value="REFSEQ_PEPTIDE_PREDICTED" selected="true">REFSEQ_PEPTIDE_PREDICTED</option>\n-                    <option value="SCHISTODB" selected="true">SCHISTODB</option>\n                     <option value="UNIGENE" selected="true">UNIGENE</option>\n                     <option value="UNIPARC" selected="true">UNIPARC</option>\n-                    <option value="UNIPATHWAY" selected="true">UNIPATHWAY</option>\n                     <option value="UNIPROT" selected="true">UNIPROT</option>\n                     <option value="WIKIGENE" selected="true">WIKIGENE</option>\n                     <option value="WORMBASE_GENE" selected="true">WORMBASE_GENE</option>\n                     <option value="WORMBASE_GSEQNAME" selected="true">WORMBASE_GSEQNAME</option>\n                     <option value="WORMBASE_LOCUS" selected="true">WORMBASE_LOCUS</option>\n+                    <option value="WORMBASE_ORTHOLOG" selected="true">WORMBASE_ORTHOLOG</option>\n                     <option value="WORMBASE_TRANSCRIPT" selected="true">WORMBASE_TRANSCRIPT</option>\n                     <option value="WORMPEP_ID" selected="true">WORMPEP_ID</option>\n                     <option value="description" selected="true">description</option>\n@@ -9204,21 +9270,19 @@\n                         <option value="NCBI_TAXONOMY_ID">NCBI_TAXONOMY_ID</option>\n                         <option value="PDB">PDB</option>\n                         <option value="PROTEIN_ID">PROTEIN_ID</option>\n-                        <option value="REACTOME">REACTOME</option>\n                         <option value="REFSEQ_MRNA">REFSEQ_MRNA</option>\n                         <option value="REFSEQ_MRNA_PREDICTED">REFSEQ_MRNA_PREDICTED</option>\n                         <option value="REFSEQ_NCRNA">REFSEQ_NCRNA</option>\n                         <option value="REFSEQ_PEPTIDE">REFSEQ_PEPTIDE</option>\n                         <option value="REFSEQ_PEPTIDE_PREDICTED">REFSEQ_PEPTIDE_PREDICTED</option>\n-                        <option value="SCHISTODB">SCHISTODB</option>\n                         <option value="UNIGENE">UNIGENE</option>\n                         <option value="UNIPARC">UNIPARC</option>\n-                        <option value="UNIPATHWAY">UNIPATHWAY</option>\n                         <option value="UNIPROT">UNIPROT</option>\n                         <option value="WIKIGENE">WIKIGENE</option>\n                         <option value="WORMBASE_GENE">WORMBASE_GENE</option>\n                         <option value="WORMBASE_GSEQNAME">WORMBASE_GSEQNAME</option>\n                         <option value="WORMBASE_LOCUS">WORMBASE_LOCUS</option>\n+                        <option value="WORMBASE_ORTHOLOG">WORMBASE_ORTHOLOG</option>\n                         <option value="WORMBASE_TRANSCRIPT">WORMBASE_TRANSCRIPT</option>\n                         <option value="WORMPEP_ID">WORMPEP_ID</option>\n                         <option value="collection">collection</option>\n'