# HG changeset patch
# User iuc
# Date 1700518518 0
# Node ID 66e23b11feaeb3ea59da411a08c81a578d56810b
# Parent  b3d99709fe1a73006820c7df5c2ef147d0c9fc2f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a

diff -r b3d99709fe1a -r 66e23b11feae macros.xml
--- a/macros.xml	Mon Aug 15 09:16:56 2022 +0000
+++ b/macros.xml	Mon Nov 20 22:15:18 2023 +0000
@@ -5,7 +5,14 @@
             <yield/>
         </requirements>
     </xml>
+    <!-- NOTE: for some tools only the version of the requirement but not the
+        tool's version is controlled by the TOOL_VERSION token 
+        (because their version is ahead of the requirement version .. 
+         please only bump the minor version in order to let the requirement
+         version catch up eventually). To find the tools check:
+        `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` -->
     <token name="@TOOL_VERSION@">1.15.1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">20.05</token>
     <token name="@FLAGS@"><![CDATA[
         #set $flags = 0
@@ -212,37 +219,7 @@
 
     <xml name="citations">
         <citations>
-            <citation type="bibtex">
-                @misc{SAM_def,
-                title={Definition of SAM/BAM format},
-                url = {https://samtools.github.io/hts-specs/},}
-            </citation>
-            <citation type="doi">10.1093/bioinformatics/btp352</citation>
-            <citation type="doi">10.1093/bioinformatics/btr076</citation>
-            <citation type="doi">10.1093/bioinformatics/btr509</citation>
-            <citation type="bibtex">
-                @misc{Danecek_et_al,
-                Author={Danecek, P., Schiffels, S., Durbin, R.},
-                title={Multiallelic calling model in bcftools (-m)},
-                url = {http://samtools.github.io/bcftools/call-m.pdf},}
-            </citation>
-            <citation type="bibtex">
-                @misc{Durbin_VCQC,
-                Author={Durbin, R.},
-                title={Segregation based metric for variant call QC},
-                url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
-            </citation>
-            <citation type="bibtex">
-                @misc{Li_SamMath,
-                Author={Li, H.},
-                title={Mathematical Notes on SAMtools Algorithms},
-                url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
-            </citation>
-            <citation type="bibtex">
-                @misc{SamTools_github,
-                title={SAMTools GitHub page},
-                url = {https://github.com/samtools/samtools},}
-            </citation>
+            <citation type="doi">10.1093/gigascience/giab008</citation>
         </citations>
     </xml>
     <xml name="version_command">
diff -r b3d99709fe1a -r 66e23b11feae samtools_fastx.xml
--- a/samtools_fastx.xml	Mon Aug 15 09:16:56 2022 +0000
+++ b/samtools_fastx.xml	Mon Nov 20 22:15:18 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>extract FASTA or FASTQ from alignment files</description>
     <macros>
         <import>macros.xml</import>
@@ -160,7 +160,7 @@
 	    <when value="yes">
                 <param name="write1st" argument="--i1" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="write first index reads to extra data set" />
                 <param name="write2nd" argument="--i2" type="boolean" truevalue="yes" falsevalue="no" checked='true' label="write second index reads to extra data set" />
-                <param name="index_format" argument="--index-format" type="text" label="Index format: How to parse barcode and quality tags">
+                <param argument="--index-format" type="text" label="Index format: How to parse barcode and quality tags">
                     <help>
 The index-format string describes how to parse the barcode and quality tags, for example:
    i14i8       the first 14 characters are index 1, the next 8 characters are index 2
@@ -171,8 +171,8 @@
                of the tag as index 1
                     </help>
                 </param>
-                <param name="barcode_tag" argument="--barcode-tag" type="text" optional="True" label="Barcode tag [default: BC]"/>
-                <param name="quality_tag" argument="--quality-tag" type="text" optional="True" label="Quality tag [default: QT]"/>
+                <param argument="--barcode-tag" type="text" optional="True" label="Barcode tag [default: BC]"/>
+                <param argument="--quality-tag" type="text" optional="True" label="Quality tag [default: QT]"/>
             </when>
         </conditional>
     </inputs>
@@ -236,7 +236,7 @@
     </outputs>
     <tests>
         <!-- tests from original Galaxy tool -->
-        <test>
+        <test expect_num_outputs="1">
             <param name="input" value="samtools_fastx-in1.bam" ftype="bam" />
             <conditional name="output_fmt_cond">
                 <param name="output_fmt_select" value="fasta" />
@@ -244,7 +244,7 @@
             <param name="outputs" value="other" />
             <output name="output" file="samtools_fastx-out1.fasta" ftype="fasta" />
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input" value="samtools_fastx-in2.bam" ftype="bam" />
             <conditional name="output_fmt_cond">
                 <param name="output_fmt_select" value="fastqsanger" />
@@ -254,7 +254,7 @@
             <output name="forward" file="samtools_fastx-out2-2.fastq" ftype="fastqsanger" />
             <output name="reverse" file="samtools_fastx-out2-3.fastq" ftype="fastqsanger" />
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input" value="samtools_fastx-in3.sam" ftype="sam" />
             <conditional name="output_fmt_cond">
                 <param name="output_fmt_select" value="fasta" />
@@ -267,7 +267,7 @@
         <!-- tests from original Galaxy tool with gz output. for some reason gzip (which is used
              for compressing stdout does not give exactly the same file contents .. the other
              compressed files seem to)-->
-        <test>
+        <test expect_num_outputs="1">
             <param name="input" value="samtools_fastx-in1.bam" ftype="bam" />
             <conditional name="output_fmt_cond">
                 <param name="output_fmt_select" value="fasta.gz" />
@@ -275,7 +275,7 @@
             <param name="outputs" value="other" />
             <output name="output" file="samtools_fastx-out1.fasta.gz" ftype="fasta.gz" decompress="true"/>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input" value="samtools_fastx-in2.bam" ftype="bam" />
             <conditional name="output_fmt_cond">
                 <param name="output_fmt_select" value="fastqsanger.gz" />
@@ -285,7 +285,7 @@
             <output name="forward" file="samtools_fastx-out2-2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
             <output name="reverse" file="samtools_fastx-out2-3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input" value="samtools_fastx-in3.sam" ftype="sam" />
             <conditional name="output_fmt_cond">
                 <param name="output_fmt_select" value="fasta.gz" />
@@ -298,7 +298,7 @@
         <!-- tests from: https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2313-->
         <!--# basic 2 output test without singleton tracking-->
         <!--test_cmd($opts, out=>'bam2fq/1.stdout.expected', out_map=>{'1.fq' => 'bam2fq/1.1.fq.expected', '2.fq' => 'bam2fq/1.2.fq.expected'},cmd=>"$$opts{bin}/samtools fastq @$threads -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.001.sam");-->
-        <test>
+        <test expect_num_outputs="3">
             <param name="input" value="bam2fq.001.sam" ftype="sam" />
             <conditional name="output_fmt_cond">
                 <param name="output_fmt_select" value="fastqsanger" />
@@ -310,7 +310,7 @@
         </test>
         <!--# basic 2 output test with singleton tracking but no singleton-->
         <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/2.1.fq.expected', '2.fq' => 'bam2fq/2.2.fq.expected', 's.fq' => 'bam2fq/2.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.001.sam");-->
-        <test>
+        <test expect_num_outputs="4">
             <param name="input" value="bam2fq.001.sam" ftype="sam" />
             <conditional name="output_fmt_cond">
                 <param name="output_fmt_select" value="fastqsanger" />
@@ -323,7 +323,7 @@
         </test>
         <!--# basic 2 output test with singleton tracking with a singleton in the middle-->
         <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/3.1.fq.expected', '2.fq' => 'bam2fq/3.2.fq.expected', 's.fq' => 'bam2fq/3.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.002.sam");-->
-        <test>
+        <test expect_num_outputs="4">
             <param name="input" value="bam2fq.002.sam" ftype="sam" />
             <conditional name="output_fmt_cond">
                 <param name="output_fmt_select" value="fastqsanger" />
@@ -336,7 +336,7 @@
         </test>
         <!--# basic 2 output test with singleton tracking with a singleton as last read-->
         <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.003.sam");-->
-        <test>
+        <test expect_num_outputs="4">
             <param name="input" value="bam2fq.003.sam" ftype="sam" />
             <conditional name="output_fmt_cond">
                 <param name="output_fmt_select" value="fastqsanger" />
@@ -349,7 +349,7 @@
         </test>
         <!--# tag output test with singleton tracking with a singleton as last read-->
         <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected', 'bc.fq' => 'bam2fq/bc.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");-->
-        <test>
+        <test expect_num_outputs="5">
             <param name="input" value="bam2fq.004.sam" ftype="sam" />
             <conditional name="output_fmt_cond">
                 <param name="output_fmt_select" value="fastqsanger" />
@@ -357,7 +357,8 @@
             <param name="outputs" value="r1,r2,s,other" />
             <conditional name="idxout_cond">
                 <param name="idxout_select" value="yes"/>
-                <param name="write1st" value="yes"/>
+                <param name="write1st" value="true"/>
+                <param name="write2nd" value="false"/>
                 <param name="barcode_tag" value="BC"/>
                 <param name="index_format" value="n2i2"/>
             </conditional>
@@ -369,7 +370,7 @@
         </test>
         <!--# test -O flag with no OQ tags-->
         <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected', 'bc.fq' => 'bam2fq/bc.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -O \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");-->
-        <test>
+        <test expect_num_outputs="5">
             <param name="input" value="bam2fq.010.sam" ftype="sam" />
             <conditional name="output_fmt_cond">
                 <param name="output_fmt_select" value="fastqsanger" />
@@ -378,7 +379,8 @@
             <param name="outputs" value="r1,r2,s,other" />
             <conditional name="idxout_cond">
                 <param name="idxout_select" value="yes"/>
-                <param name="write1st" value="yes"/>
+                <param name="write1st" value="true"/>
+                <param name="write2nd" value="false"/>
                 <param name="barcode_tag" value="BC"/>
                 <param name="index_format" value="n2i2"/>
             </conditional>
@@ -390,7 +392,7 @@
         </test>
         <!--# test -O flag with OQ tags-->
         <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/10.1.fq.expected', '2.fq' => 'bam2fq/10.2.fq.expected', 's.fq' => 'bam2fq/10.s.fq.expected', 'bc.fq' => 'bam2fq/bc10.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -O \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.010.sam");-->
-        <test>
+        <test expect_num_outputs="5">
             <param name="input" value="bam2fq.010.sam" ftype="sam" />
             <conditional name="output_fmt_cond">
                 <param name="output_fmt_select" value="fastqsanger" />
@@ -399,7 +401,8 @@
             <param name="outputs" value="r1,r2,s,other" />
             <conditional name="idxout_cond">
                 <param name="idxout_select" value="yes"/>
-                <param name="write1st" value="yes"/>
+                <param name="write1st" value="true"/>
+                <param name="write2nd" value="false"/>
                 <param name="barcode_tag" value="BC"/>
                 <param name="index_format" value="n2i2"/>
             </conditional>
@@ -411,7 +414,7 @@
         </test>
         <!--# tag output test with separators and -N flag-->
         <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/5.1.fq.expected', '2.fq' => 'bam2fq/5.2.fq.expected', 's.fq' => 'bam2fq/5.s.fq.expected', 'bc_split.fq' => 'bam2fq/bc_split.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -N \-\-index-format 'n*i*' \-\-i1 $$opts{path}/bc_split.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
-        <test>
+        <test expect_num_outputs="5">
             <param name="input" value="bam2fq.005.sam" ftype="sam" />
             <conditional name="output_fmt_cond">
                 <param name="output_fmt_select" value="fastqsanger" />
@@ -420,7 +423,8 @@
             <param name="read_numbering" value="-N"/>
             <conditional name="idxout_cond">
                 <param name="idxout_select" value="yes"/>
-                <param name="write1st" value="yes"/>
+                <param name="write1st" value="true"/>
+                <param name="write2nd" value="false"/>
                 <param name="barcode_tag" value="BC"/>
                 <param name="index_format" value="n*i*"/>
             </conditional>
@@ -432,7 +436,7 @@
         </test>
         <!--# -t flag-->
         <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/6.1.fq.expected', '2.fq' => 'bam2fq/6.2.fq.expected', 's.fq' => 'bam2fq/6.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
-        <test>
+        <test expect_num_outputs="4">
             <param name="input" value="bam2fq.005.sam" ftype="sam" />
             <conditional name="output_fmt_cond">
                 <param name="output_fmt_select" value="fastqsanger" />
@@ -447,7 +451,7 @@
         </test>
         <!--# -T flag-->
         <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/7.1.fq.expected', '2.fq' => 'bam2fq/7.2.fq.expected', 's.fq' => 'bam2fq/7.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -T MD,ia -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
-        <test>
+        <test expect_num_outputs="4">
             <param name="input" value="bam2fq.005.sam" ftype="sam" />
             <conditional name="output_fmt_cond">
                 <param name="output_fmt_select" value="fastqsanger" />
@@ -463,7 +467,7 @@
         </test>
         <!--# -i flag with no index-->
         <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/7.1.fq.expected', '2.fq' => 'bam2fq/7.2.fq.expected', 's.fq' => 'bam2fq/7.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -i -T MD,ia -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
-        <test>
+        <test expect_num_outputs="6">
             <param name="input" value="bam2fq.005.sam" ftype="sam" />
             <conditional name="output_fmt_cond">
                 <param name="output_fmt_select" value="fastqsanger" />
@@ -481,10 +485,12 @@
             <output name="reverse" file="11.2.fq.expected" ftype="fastqsanger" />
             <output name="singletons" file="11.s.fq.expected" ftype="fastqsanger" />
             <output name="output"  file="2.stdout.expected" ftype="fastqsanger" />
+            <output name="i1"  file="11.i.fq.expected" ftype="fastqsanger" />
+            <output name="i2"  file="11.i2.fq.expected" ftype="fastqsanger" />
         </test>
         <!--# -i flag with index-->
         <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/8.1.fq.expected', '2.fq' => 'bam2fq/8.2.fq.expected', 's.fq' => 'bam2fq/8.s.fq.expected', 'i.fq' => 'bam2fq/8.i.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -i \-\-index-format 'n2i2' \-\-i1 $$opts{path}/i.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");-->
-        <test>
+        <test expect_num_outputs="6">
             <param name="input" value="bam2fq.004.sam" ftype="sam" />
             <conditional name="output_fmt_cond">
                 <param name="output_fmt_select" value="fastqsanger" />
@@ -493,7 +499,7 @@
             <param name="outputs" value="r1,r2,s,other" />
             <conditional name="idxout_cond">
                 <param name="idxout_select" value="yes"/>
-                <param name="write1st" value="yes"/>
+                <param name="write1st" value="true"/>
                 <param name="barcode_tag" value="BC"/>
                 <param name="index_format" value="n2i2"/>
             </conditional>
@@ -502,6 +508,7 @@
             <output name="singletons" file="8.s.fq.expected" ftype="fastqsanger" />
             <output name="output"  file="2.stdout.expected" ftype="fastqsanger" />
             <output name="i1"  file="8.i.fq.expected" ftype="fastqsanger" />
+            <output name="i2"  file="8.i2.fq.expected" ftype="fastqsanger" />
         </test>
     </tests>
     <help><![CDATA[
diff -r b3d99709fe1a -r 66e23b11feae test-data/11.i.fq.expected
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/11.i.fq.expected	Mon Nov 20 22:15:18 2023 +0000
@@ -0,0 +1,12 @@
+@ref1_grp1_p001/1 1:N:0:AC+GT	MD:Z:10	RG:Z:grp1	BC:Z:AC-GT
+NG
++
+""
+@ref1_grp1_p002/1 1:N:0:AATT+CCGG	MD:Z:10	RG:Z:grp1	BC:Z:AATT+CCGG
+TT
++
+""
+@ref1_grp2_p001/1 1:N:0:TG+CA	MD:Z:8	RG:Z:grp2	BC:Z:TG+CA	QT:Z:ab+cd
+NC
++
++c
diff -r b3d99709fe1a -r 66e23b11feae test-data/11.i2.fq.expected
diff -r b3d99709fe1a -r 66e23b11feae test-data/8.i2.fq.expected