# HG changeset patch
# User iuc
# Date 1630482578 0
# Node ID d0f6ac9763735389e3a6e507b7750895e2dd3a9e
# Parent b93ce09eb109ce00aab82448142c2404feceeb2f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
diff -r b93ce09eb109 -r d0f6ac976373 illuminapairedend.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/illuminapairedend.xml.orig Wed Sep 01 07:49:38 2021 +0000
@@ -0,0 +1,169 @@
+<<<<<<< HEAD
+
+ Construct consensus reads from Illumina pair-end reads
+
+ macros.xml
+
+
+
+
+ fastq3p.fastq &&
+ gunzip -c '$inputfastq5p' > fastq5p.fastq &&
+ #else
+ ln -s '$inputfastq3p' fastq3p.fastq &&
+ ln -s '$inputfastq5p' fastq5p.fastq &&
+ #end if
+
+ illuminapairedend
+ ##--index-file=
+ #if $inputfastq3p.ext.startswith("fastqsolexa")
+ ##input file is in fastq nucleic format produced by solexa sequencer
+ --solexa
+ #else if $inputfastq3p.ext.startswith("fastqillumina")
+ ##input file is in fastq nucleic format produced by solexa sequencer
+ --illumina
+ #else
+ ## input file is in sanger fastq nucleic format (standard fastq)
+ --sanger
+ #end if
+ --without-progress-bar
+ --score-min='$score'
+ -r fastq3p.fastq
+ fastq5p.fastq
+ #if $inputfastq3p.ext.endswith(".gz")
+ | gzip -c
+ #end if
+ > '$output'
+ ]]>
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+=======
+
+ Construct consensus reads from Illumina pair-end reads
+
+
+ macros.xml
+
+
+
+
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+ '$output'
+
+ ]]>
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+>>>>>>> 7abad681f (add tools up until P)
diff -r b93ce09eb109 -r d0f6ac976373 macros.xml
--- a/macros.xml Mon May 10 19:32:31 2021 +0000
+++ b/macros.xml Wed Sep 01 07:49:38 2021 +0000
@@ -5,7 +5,11 @@
obitools
-
+
+
+ obitools
+
+
1.2.13
21.01
diff -r b93ce09eb109 -r d0f6ac976373 macros.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml.orig Wed Sep 01 07:49:38 2021 +0000
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+
+
+
+
+ obitools
+
+
+<<<<<<< HEAD
+
+ 1.2.13
+ 21.01
+=======
+
+
+ obitools
+
+
+ 1.2.11
+>>>>>>> 7abad681f (add tools up until P)
+
+
+
+
+
+
+
+ fastqsanger,fastqsanger.gz,fastqsolexa,fastqsolexa.gz,fasta,fasta.gz
+ input &&
+ #else
+ ln -s '$input' input &&
+ #end if
+ ]]>
+
+
+
+ > galaxy.json
+ ]]>
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+ 10.1111/1755-0998.12428
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diff -r b93ce09eb109 -r d0f6ac976373 ngsfilter.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ngsfilter.xml.orig Wed Sep 01 07:49:38 2021 +0000
@@ -0,0 +1,239 @@
+<<<<<<< HEAD
+
+ Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers
+
+ macros.xml
+
+
+
+ '$output'
+
+ #if $bool
+ #if $input.ext.endswith(".gz")
+ && gzip -c unident > '$unident'
+ #else
+ && mv unident '$unident'
+ #end if
+ #set outputs = [("output", $output), ("unident", $unident)]
+ #end if
+ @GENERATE_GALAXY_JSON@
+ ]]>
+
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+
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+ bool is True
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+=======
+
+ Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers
+
+
+ macros.xml
+
+
+
+
+ '$output'
+
+ ]]>
+
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+ bool is True
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+
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+
+
+>>>>>>> 7abad681f (add tools up until P)
diff -r b93ce09eb109 -r d0f6ac976373 obiannotate.xml
--- a/obiannotate.xml Mon May 10 19:32:31 2021 +0000
+++ b/obiannotate.xml Wed Sep 01 07:49:38 2021 +0000
@@ -1,175 +1,176 @@
-
- Adds/Edits sequence record annotations
-
- macros.xml
-
-
-
- '$output'
-
- @GENERATE_GALAXY_JSON@
- ]]>
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+ Adds/Edits sequence record annotations
+
+
+ macros.xml
+
+
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+ '$output'
+
+ @GENERATE_GALAXY_JSON@
+ ]]>
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diff -r b93ce09eb109 -r d0f6ac976373 obiannotate.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/obiannotate.xml.orig Wed Sep 01 07:49:38 2021 +0000
@@ -0,0 +1,337 @@
+<<<<<<< HEAD
+
+ Adds/Edits sequence record annotations
+
+ macros.xml
+
+
+
+ '$output'
+
+ @GENERATE_GALAXY_JSON@
+ ]]>
+
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+
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+=======
+
+ Adds/Edits sequence record annotations
+
+
+ macros.xml
+
+
+
+
+
+ '$output'
+ ]]>
+
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+
+
+
+
+
+
+>>>>>>> 7abad681f (add tools up until P)
diff -r b93ce09eb109 -r d0f6ac976373 obiclean.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/obiclean.xml.orig Wed Sep 01 07:49:38 2021 +0000
@@ -0,0 +1,156 @@
+<<<<<<< HEAD
+
+ tags a set of sequences for PCR/sequencing errors identification
+
+ macros.xml
+
+
+
+
+ '$output'
+ @GENERATE_GALAXY_JSON@
+ ]]>
+
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+=======
+
+ tags a set of sequences for PCR/sequencing errors identification
+
+
+ macros.xml
+
+
+
+
+
+
+ '$output'
+
+
+ ]]>
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+
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+
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+>>>>>>> 7abad681f (add tools up until P)
diff -r b93ce09eb109 -r d0f6ac976373 obiconvert.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/obiconvert.xml.orig Wed Sep 01 07:49:38 2021 +0000
@@ -0,0 +1,215 @@
+<<<<<<< HEAD
+
+ converts sequence files to different output formats
+
+ macros.xml
+
+
+
+ '${output}'
+ @GENERATE_GALAXY_JSON@
+ ]]>
+
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+ ecopcrdb == True
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+
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+
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+=======
+
+ converts sequence files to different output formats
+
+
+ macros.xml
+
+
+
+
+
+ '${output}'
+ ]]>
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+ ecopcrdb == True
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+
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+
+
+>>>>>>> 7abad681f (add tools up until P)
diff -r b93ce09eb109 -r d0f6ac976373 obigrep.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/obigrep.xml.orig Wed Sep 01 07:49:38 2021 +0000
@@ -0,0 +1,337 @@
+<<<<<<< HEAD
+
+ Filters sequence file
+
+ macros.xml
+
+
+
+ '$output'
+ @GENERATE_GALAXY_JSON@
+ ]]>
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+=======
+
+ Filters sequence file
+
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+ macros.xml
+
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+ '$output'
+ ]]>
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+
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+>>>>>>> 7abad681f (add tools up until P)
diff -r b93ce09eb109 -r d0f6ac976373 obisort.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/obisort.xml.orig Wed Sep 01 07:49:38 2021 +0000
@@ -0,0 +1,133 @@
+<<<<<<< HEAD
+
+ sorts sequence records according to the value of a given attribute
+
+ macros.xml
+
+
+
+
+ '$output'
+ @GENERATE_GALAXY_JSON@
+ ]]>
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+=======
+
+ sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric
+
+
+ macros.xml
+
+
+
+
+
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+ '$output'
+ ]]>
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+
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+>>>>>>> 7abad681f (add tools up until P)
diff -r b93ce09eb109 -r d0f6ac976373 obistat.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/obistat.xml.orig Wed Sep 01 07:49:38 2021 +0000
@@ -0,0 +1,288 @@
+<<<<<<< HEAD
+
+ computes basic statistics for attribute values
+
+ macros.xml
+
+
+
+ '$output'
+ ]]>
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+=======
+
+ computes basic statistics for attribute values
+
+
+ macros.xml
+
+
+
+
+
+
+ '$output'
+
+ ]]>
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+
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+
+
+>>>>>>> 7abad681f (add tools up until P)
diff -r b93ce09eb109 -r d0f6ac976373 obitab.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/obitab.xml.orig Wed Sep 01 07:49:38 2021 +0000
@@ -0,0 +1,123 @@
+<<<<<<< HEAD
+
+ converts sequence file to a tabular file
+
+ macros.xml
+
+
+
+ '$output'
+ ]]>
+
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+
+
+=======
+
+ converts sequence file to a tabular file that can be open by a spreadsheet program or R
+
+
+ macros.xml
+
+
+
+
+
+
+ '$output'
+ ]]>
+
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+
+
+
+
+
+
+>>>>>>> 7abad681f (add tools up until P)
diff -r b93ce09eb109 -r d0f6ac976373 obiuniq.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/obiuniq.xml.orig Wed Sep 01 07:49:38 2021 +0000
@@ -0,0 +1,182 @@
+<<<<<<< HEAD
+
+
+ macros.xml
+
+
+
+ '$output'
+ @GENERATE_GALAXY_JSON@
+ ]]>
+
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+=======
+
+
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+ macros.xml
+
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+ '$output'
+
+ ]]>
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+
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+
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+>>>>>>> 7abad681f (add tools up until P)