Merge in Björn's changes from galaxyproject/tools-devteam#375, update wrapper versions.

davebx · davebx · commit 7e2048a6a2ca · 2017-07-12T13:49:20.000-04:00
diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml
@@ -1,4 +1,4 @@
-<tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="@VERSION@">
+<tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="@WRAPPER_VERSION@">
     <description>chart</description>
     <expand macro="requirements" />
     <macros>
diff --git a/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml b/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml
@@ -1,9 +1,9 @@
 <tool id="cshl_fasta_formatter" version="@WRAPPER_VERSION@" name="FASTA Width">
     <description>formatter</description>
+    <expand macro="requirements" />
     <macros>
         <import>fastx_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <!--
         Note:
             fasta_formatter also has a tabular output mode (-t),
diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml
@@ -1,9 +1,9 @@
 <tool id="cshl_fasta_nucleotides_changer" version="@WRAPPER_VERSION@" name="RNA/DNA" >
     <description>converter</description>
+    <expand macro="requirements" />
     <macros>
         <import>fastx_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <command>
         <![CDATA[
         zcat -f < '$input' | fasta_nucleotide_changer -$mode -v -o '$output'
diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml
@@ -1,4 +1,4 @@
-<tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="@VERSION@">
+<tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="@WRAPPER_VERSION@">
     <description></description>
     <expand macro="requirements" />
     <macros>
diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml b/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml
@@ -1,4 +1,4 @@
-<tool id="cshl_fastq_quality_converter" name="Quality format converter" version="@VERSION@">
+<tool id="cshl_fastq_quality_converter" name="Quality format converter" version="@WRAPPER_VERSION@">
     <description>(ASCII-Numeric)</description>
     <expand macro="requirements" />
     <macros>
diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml
@@ -1,4 +1,4 @@
-<tool id="cshl_fastq_quality_filter" version="@VERSION@" name="Filter by quality">
+<tool id="cshl_fastq_quality_filter" version="@WRAPPER_VERSION@" name="Filter by quality">
     <description></description>
     <expand macro="requirements" />
     <macros>
diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml
@@ -1,4 +1,4 @@
-<tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="@VERSION@">
+<tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="@WRAPPER_VERSION@">
     <description>converter from FASTX-toolkit</description>
     <expand macro="requirements" />
     <macros>
diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml
@@ -1,4 +1,4 @@
-<tool id="cshl_fastx_artifacts_filter" version="@VERSION@" name="Remove sequencing artifacts">
+<tool id="cshl_fastx_artifacts_filter" version="@WRAPPER_VERSION@" name="Remove sequencing artifacts">
     <description></description>
     <expand macro="requirements" />
     <macros>
diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml
@@ -1,4 +1,4 @@
-<tool id="cshl_fastx_barcode_splitter" version="@VERSION@" name="Barcode Splitter">
+<tool id="cshl_fastx_barcode_splitter" version="@WRAPPER_VERSION@" name="Barcode Splitter">
     <description></description>
     <expand macro="requirements" />
     <macros>
diff --git a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml
@@ -1,4 +1,4 @@
-<tool id="cshl_fastx_clipper" name="Clip" version="@VERSOIN@">
+<tool id="cshl_fastx_clipper" name="Clip" version="1.0.2">
     <description>adapter sequences</description>
     <expand macro="requirements" />
     <macros>
diff --git a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml
@@ -1,4 +1,4 @@
-<tool id="cshl_fastx_collapser" version="@VERSION@" name="Collapse">
+<tool id="cshl_fastx_collapser" version="@WRAPPER_VERSION@" name="Collapse">
     <description>sequences</description>
     <expand macro="requirements" />
     <macros>
diff --git a/tool_collections/fastx_toolkit/fastx_macros.xml b/tool_collections/fastx_toolkit/fastx_macros.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@VERSION@">0.0.14</token>
-
+    <token name="@WRAPPER_VERSION@">1.0.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>
diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml
@@ -1,4 +1,4 @@
-<tool id="cshl_fastx_nucleotides_distribution" version="@VERSION@" name="Draw nucleotides distribution chart">
+<tool id="cshl_fastx_nucleotides_distribution" version="@WRAPPER_VERSION@" name="Draw nucleotides distribution chart">
     <description></description>
     <expand macro="requirements" />
     <macros>
diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml
@@ -1,4 +1,4 @@
-<tool id="cshl_fastx_quality_statistics" version="@VERSION@" name="Compute quality statistics">
+<tool id="cshl_fastx_quality_statistics" version="@WRAPPER_VERSION@" name="Compute quality statistics">
     <description></description>
     <expand macro="requirements" />
     <macros>
diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml
@@ -1,4 +1,4 @@
-<tool id="cshl_fastx_reverse_complement" version="@VERSION@" name="Reverse-Complement">
+<tool id="cshl_fastx_reverse_complement" version="@WRAPPER_VERSION@" name="Reverse-Complement">
     <description></description>
     <expand macro="requirements" />
     <macros>
diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml
@@ -1,4 +1,4 @@
-<tool id="cshl_fastx_trimmer" version="@VERSION@" name="Trim sequences">
+<tool id="cshl_fastx_trimmer" version="@WRAPPER_VERSION@" name="Trim sequences">
     <description></description>
     <expand macro="requirements" />
     <macros>

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="@VERSION@">`
	`1`	`+<tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="@WRAPPER_VERSION@">`
`2`	`2`	`<description>chart</description>`
`3`	`3`	`<expand macro="requirements" />`
`4`	`4`	`<macros>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="@VERSION@">`
	`1`	`+<tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="@WRAPPER_VERSION@">`
`2`	`2`	`<description></description>`
`3`	`3`	`<expand macro="requirements" />`
`4`	`4`	`<macros>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="cshl_fastq_quality_converter" name="Quality format converter" version="@VERSION@">`
	`1`	`+<tool id="cshl_fastq_quality_converter" name="Quality format converter" version="@WRAPPER_VERSION@">`
`2`	`2`	`<description>(ASCII-Numeric)</description>`
`3`	`3`	`<expand macro="requirements" />`
`4`	`4`	`<macros>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="cshl_fastq_quality_filter" version="@VERSION@" name="Filter by quality">`
	`1`	`+<tool id="cshl_fastq_quality_filter" version="@WRAPPER_VERSION@" name="Filter by quality">`
`2`	`2`	`<description></description>`
`3`	`3`	`<expand macro="requirements" />`
`4`	`4`	`<macros>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="@VERSION@">`
	`1`	`+<tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="@WRAPPER_VERSION@">`
`2`	`2`	`<description>converter from FASTX-toolkit</description>`
`3`	`3`	`<expand macro="requirements" />`
`4`	`4`	`<macros>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="cshl_fastx_artifacts_filter" version="@VERSION@" name="Remove sequencing artifacts">`
	`1`	`+<tool id="cshl_fastx_artifacts_filter" version="@WRAPPER_VERSION@" name="Remove sequencing artifacts">`
`2`	`2`	`<description></description>`
`3`	`3`	`<expand macro="requirements" />`
`4`	`4`	`<macros>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="cshl_fastx_barcode_splitter" version="@VERSION@" name="Barcode Splitter">`
	`1`	`+<tool id="cshl_fastx_barcode_splitter" version="@WRAPPER_VERSION@" name="Barcode Splitter">`
`2`	`2`	`<description></description>`
`3`	`3`	`<expand macro="requirements" />`
`4`	`4`	`<macros>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="cshl_fastx_clipper" name="Clip" version="@VERSOIN@">`
	`1`	`+<tool id="cshl_fastx_clipper" name="Clip" version="1.0.2">`
`2`	`2`	`<description>adapter sequences</description>`
`3`	`3`	`<expand macro="requirements" />`
`4`	`4`	`<macros>`