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changeset 33:87ee588b3d45 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0a8cabcc8f00014789b6d30e90be1b949d4e94d2
author iuc
date Mon, 17 Dec 2018 14:23:31 -0500
parents 4f7a5ccd2ae9
children dde39ba9c031
files maskFastaBed.xml test-data/maskFastaBed_result1.bed test-data/maskFastaBed_result1.fasta test-data/maskFastaBed_result2.bed test-data/maskFastaBed_result2.fasta test-data/maskFastaBed_result3.fasta test-data/nucBed1.fasta
diffstat 7 files changed, 29 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/maskFastaBed.xml	Tue Dec 11 14:01:26 2018 -0500
+++ b/maskFastaBed.xml	Mon Dec 17 14:23:31 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>
--- a/test-data/maskFastaBed_result1.bed	Tue Dec 11 14:01:26 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
->chr1
-GACTCATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
-NNNNNNNNNNNNNNNNNNNNAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA
-TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG
-TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA
-CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maskFastaBed_result1.fasta	Mon Dec 17 14:23:31 2018 -0500
@@ -0,0 +1,6 @@
+>chr1
+GACTCATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA
+TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG
+TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA
+CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC
--- a/test-data/maskFastaBed_result2.bed	Tue Dec 11 14:01:26 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
->chr1
-GACTCATGATttcttacctattagtggttgaacatcgtgatatgtatgttgacggccataaggctgcttcttgttgtcga
-tagaacttcatgtgcctgtaAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA
-TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG
-TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA
-CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maskFastaBed_result2.fasta	Mon Dec 17 14:23:31 2018 -0500
@@ -0,0 +1,6 @@
+>chr1
+GACTCATGATttcttacctattagtggttgaacatcgtgatatgtatgttgacggccataaggctgcttcttgttgtcga
+tagaacttcatgtgcctgtaAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA
+TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG
+TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA
+CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maskFastaBed_result3.fasta	Mon Dec 17 14:23:31 2018 -0500
@@ -0,0 +1,6 @@
+>chr1 description
+GACTCATGATttcttacctattagtggttgaacatcgtgatatgtatgttgacggccataaggctgcttcttgttgtcga
+tagaacttcatgtgcctgtaAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA
+TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG
+TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA
+CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC
--- a/test-data/nucBed1.fasta	Tue Dec 11 14:01:26 2018 -0500
+++ b/test-data/nucBed1.fasta	Mon Dec 17 14:23:31 2018 -0500
@@ -1,4 +1,4 @@
->chr1
+>chr1 description
 GACTCATGATTTCTTACCTATTAGTGGTTGAACATCGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGA
 TAGAACTTCATGTGCCTGTAAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA
 TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG