# HG changeset patch
# User iuc
# Date 1545074410 18000
# Node ID 5074e81a5ce1fa169f40fce1dc12b453fdb8a14e
# Parent  2f457890d8c8c8b9054498d66644308baea0a874
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0a8cabcc8f00014789b6d30e90be1b949d4e94d2

diff -r 2f457890d8c8 -r 5074e81a5ce1 maskFastaBed.xml
--- a/maskFastaBed.xml	Tue Dec 11 13:59:34 2018 -0500
+++ b/maskFastaBed.xml	Mon Dec 17 14:20:10 2018 -0500
@@ -25,7 +25,7 @@
         <param name="mc" type="text"  value="N"
             label="Replace masking character"
             help="That is, instead of masking with Ns, use another character. (-mc)" />
-        <param argument="-fullheader" type="boolean" truevalue="-fullheader" falsevalue=""
+        <param argument="-fullHeader" name="fullheader" type="boolean" truevalue="-fullHeader" falsevalue=""
             label="Use full fasta header." 
             help="By default, only the word before the first space or tab is used"/>
     </inputs>
@@ -37,13 +37,20 @@
             <param name="input" value="nucBed1.bed" ftype="bed" />
             <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
             <param name="soft" value="False" />
-            <output name="output" file="maskFastaBed_result1.bed" ftype="fasta" />
+            <output name="output" file="maskFastaBed_result1.fasta" ftype="fasta" />
         </test>
         <test>
             <param name="input" value="nucBed1.bed" ftype="bed" />
             <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
             <param name="soft" value="True" />
-            <output name="output" file="maskFastaBed_result2.bed" ftype="fasta" />
+            <output name="output" file="maskFastaBed_result2.fasta" ftype="fasta" />
+        </test>
+        <test>
+            <param name="input" value="nucBed1.bed" ftype="bed" />
+            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
+            <param name="soft" value="True" />
+            <param name="fullheader" value="True" />
+            <output name="output" file="maskFastaBed_result3.fasta" ftype="fasta" />
         </test>
     </tests>
     <help>
diff -r 2f457890d8c8 -r 5074e81a5ce1 test-data/maskFastaBed_result1.bed
--- a/test-data/maskFastaBed_result1.bed	Tue Dec 11 13:59:34 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
->chr1
-GACTCATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
-NNNNNNNNNNNNNNNNNNNNAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA
-TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG
-TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA
-CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC
diff -r 2f457890d8c8 -r 5074e81a5ce1 test-data/maskFastaBed_result1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maskFastaBed_result1.fasta	Mon Dec 17 14:20:10 2018 -0500
@@ -0,0 +1,6 @@
+>chr1
+GACTCATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA
+TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG
+TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA
+CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC
diff -r 2f457890d8c8 -r 5074e81a5ce1 test-data/maskFastaBed_result2.bed
--- a/test-data/maskFastaBed_result2.bed	Tue Dec 11 13:59:34 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
->chr1
-GACTCATGATttcttacctattagtggttgaacatcgtgatatgtatgttgacggccataaggctgcttcttgttgtcga
-tagaacttcatgtgcctgtaAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA
-TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG
-TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA
-CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC
diff -r 2f457890d8c8 -r 5074e81a5ce1 test-data/maskFastaBed_result2.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maskFastaBed_result2.fasta	Mon Dec 17 14:20:10 2018 -0500
@@ -0,0 +1,6 @@
+>chr1
+GACTCATGATttcttacctattagtggttgaacatcgtgatatgtatgttgacggccataaggctgcttcttgttgtcga
+tagaacttcatgtgcctgtaAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA
+TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG
+TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA
+CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC
diff -r 2f457890d8c8 -r 5074e81a5ce1 test-data/maskFastaBed_result3.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maskFastaBed_result3.fasta	Mon Dec 17 14:20:10 2018 -0500
@@ -0,0 +1,6 @@
+>chr1 description
+GACTCATGATttcttacctattagtggttgaacatcgtgatatgtatgttgacggccataaggctgcttcttgttgtcga
+tagaacttcatgtgcctgtaAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA
+TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG
+TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA
+CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC
diff -r 2f457890d8c8 -r 5074e81a5ce1 test-data/nucBed1.fasta
--- a/test-data/nucBed1.fasta	Tue Dec 11 13:59:34 2018 -0500
+++ b/test-data/nucBed1.fasta	Mon Dec 17 14:20:10 2018 -0500
@@ -1,4 +1,4 @@
->chr1
+>chr1 description
 GACTCATGATTTCTTACCTATTAGTGGTTGAACATCGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGA
 TAGAACTTCATGTGCCTGTAAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA
 TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG