# HG changeset patch
# User iuc
# Date 1661498499 0
# Node ID 79450f7fd718509605d2eea1534d22278da4abc9
# Parent  19035a7b11062c5ecf19d376154d0c3d979fda70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit c396abec691d64fc4cb7f205f54c01b1be7fd649

diff -r 19035a7b1106 -r 79450f7fd718 est-abundance.xml
--- a/est-abundance.xml	Wed Jul 06 14:47:54 2022 +0000
+++ b/est-abundance.xml	Fri Aug 26 07:21:39 2022 +0000
@@ -1,30 +1,25 @@
-<tool id="est_abundance" name="Estimate Abundance at Taxonomic Level" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>Bayesian Reestimation of Abundance with KrakEN</description>
+<tool id="est_abundance" name="Estimate Abundance at Taxonomic Level" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Bayesian Reestimation of Abundance with Kraken</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <edam_topics>
-        <edam_topic>topic_3174</edam_topic>
-        <edam_topic>topic_3697</edam_topic>
-    </edam_topics>
-    <edam_operations>
-        <edam_operation>operation_2238</edam_operation>
-    </edam_operations>
-    <xrefs>
-        <xref type="bio.tools">bracken</xref>
-    </xrefs>
-    <expand macro="requirements" />    
+    <expand macro="edam" />
+    <expand macro="xref" />
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-    est_abundance.py 
-    -i '$input' 
-    -k '$kmer_distr.fields.path' 
-    -l $level 
-    -t $threshold 
-    -o '$report'
-    ## --out-report needs to be set always, since it is written next to the input file
-    --out-report bracken.report
+        est_abundance.py
+        -i '$input'
+        -k '$kmer_distr.fields.path'
+        -l $level
+        -t $threshold
+        -o '$report'
+        ##  --out-report needs to be set always, since it is written next to the input file
+        --out-report bracken.report
+        #if $logfile_output == "True"
+            | tee '$logfile'
+        #end if
     ]]>
-    </command>    
+    </command>
     <inputs>
         <param name="input" type="data" format="tabular" label="Kraken report file" />
         <param label="Select a Kmer distribution" name="kmer_distr" type="select">
@@ -42,35 +37,42 @@
             <option value="D">Domain</option>
         </param>
         <param name="threshold" type="integer" value="10" label="Number of mismatches allowed when matching tag"
-               help="Threshold for the minimum number of reads kraken must assign to a classification for that 
+               help="Threshold for the minimum number of reads kraken must assign to a classification for that
                      classification to be considered in the final abundance estimation." />
         <param argument="--out-report" type="boolean" checked="false" label="Produce Kraken-Style Bracken report"/>
+        <param name="logfile_output" type="boolean" truevalue="True" falsevalue="False" label="Add log file output"/>
     </inputs>
     <outputs>
         <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" />
         <data name="kraken_report" format="tabular" from_work_dir="bracken.report" label="${tool.name} on ${on_string}: Kraken style report">
             <filter>out_report</filter>
         </data>
+        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file">
+            <filter> logfile_output == True </filter>
+        </data>
     </outputs>
     <tests>
         <test expect_num_outputs="1">
             <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/>
             <param name="level" value="S" />
-            <param name="bracken_database" value="test_entry"/>
+            <param name="kmer_distr" value="test_entry"/>
+            <param name="logfile_output" value="False"/>
             <output name="report" file="NC_003198.1_simulated_bracken_report.txt" ftype="tabular"/>
         </test>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="3">
             <param name="input" value="NC_011750.1_simulated_kraken_report.txt" ftype="tabular"/>
             <param name="level" value="S" />
-            <param name="bracken_database" value="test_entry"/>
+            <param name="kmer_distr" value="test_entry"/>
             <param name="out_report" value="true"/>
+            <param name="logfile_output" value="True"/>
             <output name="report" file="NC_011750.1_simulated_bracken_report.txt" ftype="tabular"/>
             <output name="kraken_report" file="NC_011750.1_simulated_kraken_style_bracken_report.txt" ftype="tabular"/>
+            <output name="logfile" file="test2.log" lines_diff="8" />
         </test>
     </tests>
     <help>
     <![CDATA[
-        Documentation can be found at `site <http://ccb.jhu.edu/software/bracken/index.shtml?t=manual>`_.
+        Documentation can be found at `site <http://ccb.jhu.edu/software/bracken/index.shtml?t=manual>`
     ]]></help>
     <expand macro="citations" />
 </tool>
diff -r 19035a7b1106 -r 79450f7fd718 macros.xml
--- a/macros.xml	Wed Jul 06 14:47:54 2022 +0000
+++ b/macros.xml	Fri Aug 26 07:21:39 2022 +0000
@@ -1,6 +1,7 @@
 <macros>
     <token name="@TOOL_VERSION@">2.7</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@PROFILE@">21.05</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bracken</requirement>
@@ -9,6 +10,20 @@
     <xml name="version">
         <version_command>echo @TOOL_VERSION@</version_command>
     </xml>
+    <xml name="edam">
+        <edam_topics>
+            <edam_topic>topic_3174</edam_topic>
+            <edam_topic>topic_3697</edam_topic>
+        </edam_topics>
+        <edam_operations>
+            <edam_operation>operation_2238</edam_operation>
+        </edam_operations>
+    </xml>
+    <xml name="xref">
+        <xrefs>
+            <xref type="bio.tools">bracken</xref>
+        </xrefs>
+    </xml>
     <xml name="citations">
         <citations>
             <citation type="doi">10.7717/peerj-cs.104</citation>
diff -r 19035a7b1106 -r 79450f7fd718 test-data/NC_003198.1_simulated_kraken_style_bracken_report.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_003198.1_simulated_kraken_style_bracken_report.txt	Fri Aug 26 07:21:39 2022 +0000
@@ -0,0 +1,9 @@
+100.00	42	0	R	1	root
+100.00	42	0	R1	131567	  cellular organisms
+100.00	42	0	D	2	    Bacteria
+100.00	42	0	P	1224	      Proteobacteria
+100.00	42	0	C	1236	        Gammaproteobacteria
+100.00	42	0	O	91347	          Enterobacterales
+100.00	42	0	F	543	            Enterobacteriaceae
+100.00	42	0	G	590	              Salmonella
+100.00	42	42	S	28901	                Salmonella enterica
diff -r 19035a7b1106 -r 79450f7fd718 test-data/test2.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2.log	Fri Aug 26 07:21:39 2022 +0000
@@ -0,0 +1,14 @@
+PROGRAM START TIME: 08-05-2022 14:41:48
+BRACKEN SUMMARY (Kraken report: /tmp/tmpy56dgetr/files/f/5/4/dataset_f5412c50-3888-4466-b041-32814cdda47c.dat)
+    >>> Threshold: 10 
+    >>> Number of species in sample: 1 
+	  >> Number of species with reads > threshold: 1 
+	  >> Number of species with reads < threshold: 0 
+    >>> Total reads in sample: 45
+	  >> Total reads kept at species level (reads > threshold): 42
+	  >> Total reads discarded (species reads < threshold): 0
+	  >> Reads distributed: 1
+	  >> Reads not distributed (eg. no species above threshold): 0
+	  >> Unclassified reads: 2
+BRACKEN OUTPUT PRODUCED: /tmp/tmpy56dgetr/job_working_directory/000/4/outputs/galaxy_dataset_e099cc44-07e6-4507-b11f-137722113078.dat
+PROGRAM END TIME: 08-05-2022 14:41:48