# HG changeset patch
# User iuc
# Date 1685553317 0
# Node ID 8a477224dfee040e548e281be497f18c0d48fd71
# Parent  ae36fab06bc2a0ded02e0c2b8be359ba7a1435bc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 3a5a4ad75547c6c27430d85e6ddf3c2ff1ece0ba

diff -r ae36fab06bc2 -r 8a477224dfee samtools_coverage.xml
--- a/samtools_coverage.xml	Mon Aug 15 09:15:40 2022 +0000
+++ b/samtools_coverage.xml	Wed May 31 17:15:17 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_coverage" name="Samtools coverage" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="samtools_coverage" name="Samtools coverage" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>computes the depth at each position or region</description>
     <macros>
         <import>macros.xml</import>
@@ -7,11 +7,15 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @PREPARE_IDX@
+        #if $condition_input.input_pooling == "No":
+            @PREPARE_IDX@
+        #else:
+            @PREPARE_IDX_MULTIPLE@
+        #end if
         samtools coverage
 
             #if $condition_input.input_pooling == "Yes":
-                ${ ' '.join( [ "'%s'" %  $x for $x in $condition_input.input] ) }
+                ${ ' '.join( [ "'%s'" %  $x for $x in $condition_input.input_bams] ) }
             #else
                 '$condition_input.input'
             #end if
@@ -22,11 +26,11 @@
 
             #set $filter = $additional_options.required_flags
             @FLAGS@
-            -rf $flags
+            --rf $flags
 
             #set $filter = $additional_options.skipped_flags
             @FLAGS@
-            -ff $flags
+            --ff $flags
 
             #if $condition_histogram.histogram_select == "yes"
                 -m
@@ -45,10 +49,10 @@
                 <option value="Yes">Yes</option>
             </param>
             <when value="No" >
-                <param name="input" type="data" format="bam" multiple="true" label="BAM file"/>
+                <param name="input" type="data" format="bam" label="BAM file"/>
             </when>
             <when value="Yes">
-                <param name="input" type="data" format="bam" multiple="true" label="BAM files to be pooled"/>
+                <param name="input_bams" type="data" format="bam" multiple="true" label="BAM files to be pooled"/>
             </when>
         </conditional>
 
@@ -96,7 +100,7 @@
         </test>
         <test>
             <param name="input_pooling" value="Yes" />
-            <param name="input" value="test_1.bam,test_2.bam" ftype="bam" />
+            <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" />
             <param name="histogram_select" value="yes" />
             <param name="n_bins" value="100" />
             <output name="output" file="results_3.txt" ftype="tabular" />
diff -r ae36fab06bc2 -r 8a477224dfee test-data/results_1.tabular
--- a/test-data/results_1.tabular	Mon Aug 15 09:15:40 2022 +0000
+++ b/test-data/results_1.tabular	Wed May 31 17:15:17 2023 +0000
@@ -0,0 +1,5 @@
+#rname	startpos	endpos	numreads	covbases	coverage	meandepth	meanbaseq	meanmapq
+insert	1	599	2	20	3.3389	0.033389	32	30
+ref1	1	45	6	31	68.8889	1.24444	255	30
+ref2	1	40	6	36	90	3.375	63.3	30
+ref3	1	4	0	0	0	0	0	0
diff -r ae36fab06bc2 -r 8a477224dfee test-data/results_2.txt
--- a/test-data/results_2.txt	Mon Aug 15 09:15:40 2022 +0000
+++ b/test-data/results_2.txt	Wed May 31 17:15:17 2023 +0000
@@ -0,0 +1,38 @@
+insert (599bp)
+>  73.64% │       █                                          │ Number of reads: 2
+>  65.45% │       █                                          │ 
+>  57.27% │       █                                          │ Covered bases:   20bp
+>  49.09% │    ▅  █                                          │ Percent covered: 3.339%
+>  40.91% │    █  █                                          │ Mean coverage:   0.0334x
+>  32.73% │    █▄ █                                          │ Mean baseQ:      32
+>  24.55% │    ██ █                                          │ Mean mapQ:       30
+>  16.36% │    ██ █                                          │ 
+>   8.18% │    ██ █▁                                         │ Histo bin width: 11bp
+>   0.00% │    ██ ██                                         │ Histo max bin:   81.818%
+          1        110       220       330       440        599   
+
+ref1 (45bp)
+>  90.00% │      ████████████████      █████  ██████████│ Number of reads: 6
+>  80.00% │      ████████████████      █████  ██████████│ 
+>  70.00% │      ████████████████      █████  ██████████│ Covered bases:   31bp
+>  60.00% │      ████████████████      █████  ██████████│ Percent covered: 68.89%
+>  50.00% │      ████████████████      █████  ██████████│ Mean coverage:   1.24x
+>  40.00% │      ████████████████      █████  ██████████│ Mean baseQ:      255
+>  30.00% │      ████████████████      █████  ██████████│ Mean mapQ:       30
+>  20.00% │      ████████████████      █████  ██████████│ 
+>  10.00% │      ████████████████      █████  ██████████│ Histo bin width: 1bp
+>   0.00% │      ████████████████      █████  ██████████│ Histo max bin:   100%
+          1         10        20        30             45   
+
+ref2 (40bp)
+>  90.00% │████████████████████████████████████    │ Number of reads: 6
+>  80.00% │████████████████████████████████████    │ 
+>  70.00% │████████████████████████████████████    │ Covered bases:   36bp
+>  60.00% │████████████████████████████████████    │ Percent covered: 90%
+>  50.00% │████████████████████████████████████    │ Mean coverage:   3.38x
+>  40.00% │████████████████████████████████████    │ Mean baseQ:      63.3
+>  30.00% │████████████████████████████████████    │ Mean mapQ:       30
+>  20.00% │████████████████████████████████████    │ 
+>  10.00% │████████████████████████████████████    │ Histo bin width: 1bp
+>   0.00% │████████████████████████████████████    │ Histo max bin:   100%
+          1         10        20        30         40   
diff -r ae36fab06bc2 -r 8a477224dfee test-data/results_3.txt
--- a/test-data/results_3.txt	Mon Aug 15 09:15:40 2022 +0000
+++ b/test-data/results_3.txt	Wed May 31 17:15:17 2023 +0000
@@ -0,0 +1,38 @@
+insert (599bp)
+>  90.00% │          █     █                                                                                   │ Number of reads: 4
+>  80.00% │          █     █                                                                                   │ 
+>  70.00% │          ██    ██                                                                                  │ Covered bases:   20bp
+>  60.00% │          ██    ██                                                                                  │ Percent covered: 3.339%
+>  50.00% │          ██    ██                                                                                  │ Mean coverage:   0.0668x
+>  40.00% │          ██    ██                                                                                  │ Mean baseQ:      32
+>  30.00% │          ██    ██                                                                                  │ Mean mapQ:       30
+>  20.00% │          ██    ██                                                                                  │ 
+>  10.00% │         ███   ███                                                                                  │ Histo bin width: 5bp
+>   0.00% │         ███   ███                                                                                  │ Histo max bin:   100%
+          1         50       100       150       200       250       300       350       400       450        599   
+
+ref1 (45bp)
+>  90.00% │      ████████████████      █████  ██████████│ Number of reads: 12
+>  80.00% │      ████████████████      █████  ██████████│ 
+>  70.00% │      ████████████████      █████  ██████████│ Covered bases:   31bp
+>  60.00% │      ████████████████      █████  ██████████│ Percent covered: 68.89%
+>  50.00% │      ████████████████      █████  ██████████│ Mean coverage:   2.49x
+>  40.00% │      ████████████████      █████  ██████████│ Mean baseQ:      255
+>  30.00% │      ████████████████      █████  ██████████│ Mean mapQ:       30
+>  20.00% │      ████████████████      █████  ██████████│ 
+>  10.00% │      ████████████████      █████  ██████████│ Histo bin width: 1bp
+>   0.00% │      ████████████████      █████  ██████████│ Histo max bin:   100%
+          1         10        20        30             45   
+
+ref2 (40bp)
+>  90.00% │████████████████████████████████████    │ Number of reads: 12
+>  80.00% │████████████████████████████████████    │ 
+>  70.00% │████████████████████████████████████    │ Covered bases:   36bp
+>  60.00% │████████████████████████████████████    │ Percent covered: 90%
+>  50.00% │████████████████████████████████████    │ Mean coverage:   6.75x
+>  40.00% │████████████████████████████████████    │ Mean baseQ:      63.3
+>  30.00% │████████████████████████████████████    │ Mean mapQ:       30
+>  20.00% │████████████████████████████████████    │ 
+>  10.00% │████████████████████████████████████    │ Histo bin width: 1bp
+>   0.00% │████████████████████████████████████    │ Histo max bin:   100%
+          1         10        20        30         40