diff tools/primers/seq_primer_clip.xml @ 1:8c02a91a8680 draft

Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.

--- a/tools/primers/seq_primer_clip.xml	Mon Apr 29 06:11:00 2013 -0400
+++ b/tools/primers/seq_primer_clip.xml	Tue Apr 30 11:04:43 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.8">
+<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.9">
     <description>Trim off 5' or 3' primers</description>
     <version_command interpreter="python">seq_primer_clip.py --version</version_command>   
     <command interpreter="python">
@@ -39,58 +39,58 @@
     </outputs>
     <tests>
         <test>
-            <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30.fasta" ftype="fasta" />
-            <param name="primer_fasta" value="primers/dop_primers.fasta" />
+            <param name="input_file" value="MID4_GLZRM4E04_rnd30.fasta" ftype="fasta" />
+            <param name="primer_fasta" value="dop_primers.fasta" />
             <param name="primer_type" value="Forward" />
             <param name="mm" value="2" />
             <param name="keep_negatives" value="false" />
             <param name="min_len" value="35" />
-            <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" />
+            <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" />
         </test>
         <test>
-            <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30.fastqsanger" ftype="fastqsanger" />
-            <param name="primer_fasta" value="primers/dop_primers.fasta" />
+            <param name="input_file" value="MID4_GLZRM4E04_rnd30.fastqsanger" ftype="fastqsanger" />
+            <param name="primer_fasta" value="dop_primers.fasta" />
             <param name="primer_type" value="Forward" />
             <param name="mm" value="2" />
             <param name="keep_negatives" value="false" />
             <param name="min_len" value="35" />
-            <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" />
+            <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" />
         </test>
         <test>
-            <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30.sff" ftype="sff" />
-            <param name="primer_fasta" value="primers/dop_primers.fasta" />
+            <param name="input_file" value="MID4_GLZRM4E04_rnd30.sff" ftype="sff" />
+            <param name="primer_fasta" value="dop_primers.fasta" />
             <param name="primer_type" value="Forward" />
             <param name="mm" value="2" />
             <param name="keep_negatives" value="false" />
             <param name="min_len" value="35" />
-            <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" />
+            <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" />
         </test>
         <test>
-            <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" />
-            <param name="primer_fasta" value="primers/dop_primers.fasta" />
+            <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" />
+            <param name="primer_fasta" value="dop_primers.fasta" />
             <param name="primer_type" value="Reverse" />
             <param name="mm" value="2" />
             <param name="keep_negatives" value="true" />
             <param name="min_len" value="35" />
-            <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_frclip.fasta" ftype="fasta" />
+            <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.fasta" ftype="fasta" />
         </test>
         <test>
-            <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" />
-            <param name="primer_fasta" value="primers/dop_primers.fasta" />
+            <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" />
+            <param name="primer_fasta" value="dop_primers.fasta" />
             <param name="primer_type" value="Reverse" />
             <param name="mm" value="2" />
             <param name="keep_negatives" value="true" />
             <param name="min_len" value="35" />
-            <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger" ftype="fastqsanger" />
+            <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.fastqsanger" ftype="fastqsanger" />
         </test>
         <test>
-            <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" />
-            <param name="primer_fasta" value="primers/dop_primers.fasta" />
+            <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" />
+            <param name="primer_fasta" value="dop_primers.fasta" />
             <param name="primer_type" value="Reverse" />
             <param name="mm" value="2" />
             <param name="keep_negatives" value="true" />
             <param name="min_len" value="35" />
-            <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" />
+            <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" />
         </test>
     </tests>
     <requirements>