diff multiqc.xml @ 12:a7e3e7e1019c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984

--- a/multiqc.xml	Mon Aug 06 10:41:37 2018 -0400
+++ b/multiqc.xml	Wed Aug 08 08:49:10 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.2">
+<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@">
     <description>aggregate results from bioinformatics analyses into a single report</description>
     <macros>
-        <token name="@WRAPPER_VERSION@">1.5</token>
+        <token name="@WRAPPER_VERSION@">1.6</token>
         <token name="@ESCAPE_IDENTIFIER@">
 <![CDATA[
 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
@@ -156,6 +156,14 @@
                 @LN_2_FILES@
             #end if
         #end for
+    #elif str($repeat.software_cond.software) == "fastp"
+        #set $pattern = "report_title"
+        #for $file in $repeat.software_cond.input
+            @ESCAPE_IDENTIFIER@
+            #set file_path = os.path.join($software_dir, str($identifier) + 'fastp.json')
+            ln -s '$file' '$file_path' &&
+            grep -q "$pattern" '$file_path' || die "'$pattern' or 'report_title' not found in the file" &&
+        #end for
     #elif str($repeat.software_cond.software) == "fastqc"
         #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
             @CREATE_REPEAT_DIR_1@
@@ -499,6 +507,7 @@
                     <option value="deeptools">deepTools</option>
                     <!--<option value="disambiguate">Disambiguate</option>-->
                     <!--<option value="fastq_screen">FastQ Screen</option>-->
+                    <option value="fastp">fastp</option>
                     <option value="fastqc">FastQC</option>
                     <option value="featureCounts">featureCounts</option>
                     <option value="flexbar">Flexbar</option>
@@ -584,6 +593,9 @@
                         <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/>
                     </repeat>
                 </when>
+                <when value="fastp">
+                    <param name="input" type="data" format="json" multiple="true" label="Output of fastp" help="It should be the json report from fastp containing 'report_title'"/>
+                </when>
                 <when value="fastqc">
                     <repeat name="output" title="FastQC output" min="1">
                         <param name="type" type="select" label="Type of FastQC output?">
@@ -813,6 +825,12 @@
             </repeat>
             <repeat name="results">
                 <conditional name="software_cond">
+                    <param name="software" value="fastp" />
+                    <param name="input" value="fastp1.json.txt,fastp2.json.txt" />
+                </conditional>
+            </repeat>
+            <repeat name="results">
+                <conditional name="software_cond">
                     <param name="software" value="fastqc" />
                     <repeat name="output">
                         <param name="type" value="data"/>
@@ -846,6 +864,7 @@
                     <has_text text="Title of the report" />
                     <has_text text="Commment for the report" />
                     <has_text text="cutadapt_plot" />
+                    <has_text text="An ultra-fast all-in-one FASTQ preprocessor" />
                     <has_text text="fastqc_seq_heatmap_key_t" />
                     <has_text text="flexbar_plot" />
                     <has_text text="sortmerna-detailed-plot" />
@@ -855,6 +874,7 @@
             <output name="log" file="pre_alignment_soft_log.txt" compare="sim_size"/>
             <output_collection name="stats" type="list">
                 <element name="cutadapt" file="cutadapt_stats.tabular" compare="sim_size" delta="10"/>
+                <element name="fastp" file="fastp_stats.tabular" compare="sim_size" delta="10"/>
                 <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/>
                 <element name="flexbar" file="flexbar_stats.tabular" compare="sim_size" delta="10"/>
                 <element name="general_stats" file="pre_alignment_soft_stats.tabular" compare="sim_size" delta="30"/>