diff hicQuickQC.xml @ 6:9c5078f3926b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"

--- a/hicQuickQC.xml	Fri Dec 11 21:05:59 2020 +0000
+++ b/hicQuickQC.xml	Tue Mar 16 15:08:31 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicquickqc" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hicquickqc" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>get a first quality estimate of Hi-C data</description>
     <macros>
         <token name="@BINARY@">hicQuickQC</token>
@@ -16,6 +16,8 @@
                 '${repeat.samFile}'
             #end for
 
+            --restrictionCutFile '$restrictionCutFile'
+            
             #if $restrictionSequence:
                 --restrictionSequence '$restrictionSequence'
             #end if
@@ -30,56 +32,43 @@
         && mv ./QCfolder/* $qc.files_path/
         && mv $qc.files_path/hicQC.html $qc
         && mv $qc.files_path/*.log raw_qc
-    ]]></command>
+    ]]>    </command>
     <inputs>
-         <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)"
-                help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file.">
-            <param name="samFile" type="data" format="sam,qname_input_sorted.bam"/>
+        <!-- can we use multiple="true" with min="2" and max="2" ? -->
+        <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file.">
+            <param name="samFile" type="data" format="sam,qname_input_sorted.bam" />
         </repeat>
-
-        <param argument="--restrictionSequence" type="text" optional="true" label="Sequence of the restriction site"
-            help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
-            &quot;dangling-ends&quot;. If not given, such statistics will not be available." />
+        <expand macro="restrictionCutFile" />
+        <expand macro="restrictionSequence" />
+        <expand macro="danglingSequence" />
 
-        <param argument="--danglingSequence" type="text" optional="true" label="Dangling sequence"
-            help="Sequence left by the restriction enzyme after cutting.
-                    Each restriction enzyme recognizes a different DNA sequence and,
-                    after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence.
-                    For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT.
-                    For DpnII, the restriction site and dangling end sequence are the same: GATC.
-                    This information is easily found on the description of the restriction enzyme.
-                    The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads.
-                    A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. "/>
-
-        <param argument="--lines" optional='true'  type="integer" label="Lines" help= "Number of lines to consider for the qc test run." value='1000000'/>
+        <param argument="--lines" optional='true' type="integer" label="Lines to analyze for the QC report" help= "Number of lines to consider for the qc test run." value='1000000' />
 
     </inputs>
     <outputs>
-       <data name="qc" format="html" label="${tool.name} QC on ${on_string}"/>
-       <data name="raw_qc" from_work_dir='raw_qc' format='txt' label="${tool.name} raw QC on ${on_string}" />
+        <data name="qc" format="html" label="${tool.name} QC on ${on_string}" />
+        <data name="raw_qc" from_work_dir='raw_qc' format='txt' label="${tool.name} raw QC on ${on_string}" />
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <repeat name="samFiles">
-                <param name="samFile" value="small_test_R1_unsorted.sam"/>
+                <param name="samFile" value="small_test_R1_unsorted.sam" />
             </repeat>
             <repeat name="samFiles">
-                <param name="samFile" value="small_test_R2_unsorted.sam"/>
+                <param name="samFile" value="small_test_R2_unsorted.sam" />
             </repeat>
-            <conditional name="restrictionCutFileBinSize_conditional">
-                <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/>
-                <repeat name='binSizes'>
-                    <param name="binSize" value="5000"/>
-                </repeat>
-            </conditional>
-            <param name="lines" value='1000'/>
-            <output name="raw_qc" file='hicQuickQC/QC.log' compare='diff' lines_diff='2'/>
+            <param name='restrictionCutFile' value='DpnII_10k.bed' />
+            <param name='restrictionSequence' value='GATC' />
+            <param name='danglingSequence' value='GATC' />
+
+            <param name="lines" value='1000' />
+            <output name="raw_qc" file='hicQuickQC/QC.log' compare='diff' lines_diff='2' />
         </test>
     </tests>
     <help><![CDATA[
 
 Quick QC
-====================
+========
 
 Get a quick impression on the quality of your Hi-C data. hicQuickQC considers the first n lines of two bam/sam files to get a first estimate of the quality of the data. It is highly recommended to set the restriction enzyme and dangling end parameter to get a good quality report.
 
@@ -88,6 +77,6 @@
 For more information about HiCExplorer please consider our documentation on readthedocs.io_
 
 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
-]]></help>
+]]>    </help>
     <expand macro="citations" />
 </tool>