# HG changeset patch
# User iuc
# Date 1475494568 14400
# Node ID c78cf6fe3018f142f2198394a8642be1ebf90a98
# Parent  2ab422b551df8d97778ce5b56ec8869fc23723b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6

diff -r 2ab422b551df -r c78cf6fe3018 all_fasta.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/all_fasta.loc.sample	Mon Oct 03 07:36:08 2016 -0400
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
diff -r 2ab422b551df -r c78cf6fe3018 bamToFastq.xml
--- a/bamToFastq.xml	Wed Sep 14 17:30:10 2016 -0400
+++ b/bamToFastq.xml	Mon Oct 03 07:36:08 2016 -0400
@@ -16,8 +16,8 @@
     </command>
     <inputs>
         <param format="bam" name="input" type="data" label="Convert the following BAM file to FASTQ"/>
-        <param name="tags" type="boolean" truevalue="-tags" falsevalue="" selected="False" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/>
-        <param name="fq2" type="boolean" truevalue="-fq2" falsevalue="" selected="False" label="FASTQ for second end.
+        <param name="tags" type="boolean" truevalue="-tags" falsevalue="" checked="False" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/>
+        <param name="fq2" type="boolean" truevalue="-fq2" falsevalue="" checked="False" label="FASTQ for second end.
             Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/>
     </inputs>
     <outputs>
diff -r 2ab422b551df -r c78cf6fe3018 getfastaBed.xml
--- a/getfastaBed.xml	Wed Sep 14 17:30:10 2016 -0400
+++ b/getfastaBed.xml	Mon Oct 03 07:36:08 2016 -0400
@@ -7,19 +7,38 @@
     <expand macro="stdio" />
     <command>
 <![CDATA[
+        #if str( $fasta_source.fasta_source_selector ) == 'history':
+          #set $fasta_file = $fasta_source.fasta
+        #else
+          #set $fasta_file = $fasta_source.fasta_id.fields.path
+        #end if
         bedtools getfasta
         $name
         $tab
         $strand
         $split
-        -fi $fasta 
-        -bed $input
-        -fo $output
+        -fi '$fasta_file'
+        -bed '$input'
+        -fo '$output'
 ]]>
     </command>
     <inputs>
         <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" />
-        <param format="fasta" name="fasta" type="data" label="Fasta file" />
+        
+        <conditional name="fasta_source">
+            <param name="fasta_source_selector" type="select" label="Choose the source for the fasta file">
+                <option value="history" selected="True">History</option>
+                <option value="preloaded">Server indexed files</option>
+            </param>
+            <when value="history">
+                <param name="fasta" format="fasta" type="data" label="Fasta file" />
+            </when>
+            <when value="preloaded">
+               <param name="fasta_id" type="select">
+                  <options from_data_table="all_fasta" />
+               </param> 
+            </when>
+        </conditional>
         <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue=""
             label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file"
             help="(-name)" />
diff -r 2ab422b551df -r c78cf6fe3018 maskFastaBed.xml
--- a/maskFastaBed.xml	Wed Sep 14 17:30:10 2016 -0400
+++ b/maskFastaBed.xml	Mon Oct 03 07:36:08 2016 -0400
@@ -21,7 +21,7 @@
         <param name="soft" type="boolean" checked="false" truevalue="-soft" falsevalue=""
             label="Soft-mask (that is, convert to lower-case bases) the FASTA sequence"
             help="By default, hard-masking (that is, conversion to Ns) is performed. (-soft)" />
-        <param name="mc" type="text"  value="N" length="1"
+        <param name="mc" type="text"  value="N"
             label="Replace masking character"
             help="That is, instead of masking with Ns, use another character. (-mc)" />
     </inputs>
diff -r 2ab422b551df -r c78cf6fe3018 multiCov.xml
--- a/multiCov.xml	Wed Sep 14 17:30:10 2016 -0400
+++ b/multiCov.xml	Mon Oct 03 07:36:08 2016 -0400
@@ -55,7 +55,7 @@
     <tests>
         <test>
             <param name="input" value="multiCov1.bed" ftype="bed" />
-            <param name="bams" value="srma_in3.bam,srma_in3.bam" ftpye="bam"/>
+            <param name="bams" value="srma_in3.bam,srma_in3.bam" ftype="bam"/>
             <param name="q" value="1"/>
             <param name="split" value="False"/>
             <output name="output" file="multiCovBed_result1.bed" ftype="bed" />
diff -r 2ab422b551df -r c78cf6fe3018 shuffleBed.xml
--- a/shuffleBed.xml	Wed Sep 14 17:30:10 2016 -0400
+++ b/shuffleBed.xml	Mon Oct 03 07:36:08 2016 -0400
@@ -30,9 +30,9 @@
     </command>
     <inputs>
         <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
-        <param name="bedpe" type="boolean" label="The file is in BEDPE format" selected="False" truevalue="-bedpe" falsevalue="" />
+        <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" />
         <expand macro="genome" />
-        <param name="chrom" type="boolean" selected="False" truevalue="-chrom" falsevalue=""
+        <param name="chrom" type="boolean" checked="False" truevalue="-chrom" falsevalue=""
             label="Keep features in the input file on the same chromosome"
             help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen. (-chrom)" />
         <expand macro="seed" />
@@ -51,14 +51,14 @@
                 <param name="incl" type="data" format="bed" label="Choose File" />
             </when>
         </conditional>
-        <param name="chromfirst" type="boolean" selected="False" truevalue="-chromFirst" falsevalue="" 
+        <param name="chromfirst" type="boolean" checked="False" truevalue="-chromFirst" falsevalue="" 
             label="Choose chromosome first"
             help="Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size. (-chromFirst)" />
         <param name="maxtries" type="integer" value="1000"
             label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" help="(-maxTries)" />
-        <param name="no_overlap" type="boolean" selected="False" truevalue="-noOverlapping" falsevalue=""
+        <param name="no_overlap" type="boolean" checked="False" truevalue="-noOverlapping" falsevalue=""
             label="Don’t allow shuffled intervals to overlap" help="(-noOverlapping)" />
-        <param name="allow_beyond" type="boolean" selected="False" truevalue="-allowBeyondChromEnd" falsevalue=""
+        <param name="allow_beyond" type="boolean" checked="False" truevalue="-allowBeyondChromEnd" falsevalue=""
             label="Allow the original the length of the original records to extebd beyond the length of the chromosome" help="(-allowBeyondChromEnd)" />
     </inputs>
     <outputs>
diff -r 2ab422b551df -r c78cf6fe3018 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Oct 03 07:36:08 2016 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+</tables>
diff -r 2ab422b551df -r c78cf6fe3018 unionBedGraphs.xml
--- a/unionBedGraphs.xml	Wed Sep 14 17:30:10 2016 -0400
+++ b/unionBedGraphs.xml	Mon Oct 03 07:36:08 2016 -0400
@@ -105,9 +105,6 @@
 
 This tool merges multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files.
 
-.. image:: http://people.virginia.edu/~arq5x/files/bedtools-galaxy/ubg.png
-
-
 .. class:: warningmark
 
 This tool requires that each BedGraph file is reference-sorted (chrom, then start) and contains non-overlapping intervals (within a given file).