diff samtools_view.xml @ 14:5826298f6a73 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e

--- a/samtools_view.xml	Sun Dec 19 15:58:19 2021 +0000
+++ b/samtools_view.xml	Mon Aug 15 09:19:43 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
+<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>- reformat, filter, or subsample SAM, BAM or CRAM</description>
     <macros>
         <import>macros.xml</import>
@@ -154,11 +154,11 @@
                         ## not dealing with all of the reads in the indexed
                         ## file. We have to do an extra pass over the input to
                         ## count the reads to subsample.
-                        sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {frac=s/${mode.subsample_config.subsampling_mode.target}; print(frac > 1 ? $seed+1/frac : ".0")}'` &&
+                        sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {frac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", frac > 1 ? $seed+1/frac : ".0")}'` &&
                     #else:
                         ## We can get the count of reads to subsample using
                         ## an inexpensive call to idxstats.
-                        sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=s/${mode.subsample_config.subsampling_mode.target}; print(frac > 1 ? $seed+1/frac : ".0")}'` &&
+                        sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", frac > 1 ? $seed+1/frac : ".0")}'` &&
                     #end if
                 #end if
             #end if
@@ -690,7 +690,7 @@
             </conditional>
             <output name="outputsam" file="test_20.bam" ftype="bam" lines_diff="4" />
         </test>
-        <!-- 21) sampling options-->
+        <!-- 21) sampling options target < total reads -->
         <test>
             <param name="input" value="in_test_15.sam" ftype="sam" />
             <conditional name="mode">
@@ -707,9 +707,9 @@
                     </conditional>
                 </conditional>
             </conditional>
-            <output name="outputsam" file="test_21.sam" ftype="sam" compare="diff" lines_diff="6" />
+            <output name="outputsam" file="test_21.sam" ftype="sam" compare="diff" lines_diff="10" />
         </test>
-        <!-- 22) -->
+        <!-- 22) target > total reads -->
         <test>
             <param name="input" value="in_test_15.sam" ftype="sam" />
             <conditional name="mode">
@@ -786,7 +786,7 @@
                     </conditional>
                 </conditional>
             </conditional>
-            <output name="outputsam" file="test_25.sam" ftype="sam" compare="diff" lines_diff="6" />
+            <output name="outputsam" file="test_25.sam" ftype="sam" compare="diff" lines_diff="2" />
         </test>
         <!-- 26) -->
         <test>