diff macros_process.xml @ 4:60c1c4d7d2c1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty

--- a/macros_process.xml	Fri Jan 04 03:33:00 2019 -0500
+++ b/macros_process.xml	Wed Feb 27 09:53:30 2019 -0500
@@ -3,60 +3,10 @@
 <!-- macros and tokens for process_radtags and process_short_reads -->
 
 <macros>
-    <!-- fastq input for process_radtags/shortreads-->
-    <xml name="process_inputs">
-        <conditional name="input_type">
-            <param name="options_type_selector" type="select" label="Single-end or paired-end reads files">
-                <option value="single" selected="True">Single-end files</option>
-                <option value="paired">Paired-end files</option>
-            </param>
-            <when value="single">
-                <param name="fqinputs" argument="-f" format="fastqsanger,fastqsanger.gz" multiple="true" type="data" label="singles-end reads infile(s)" help="input files" />
-                <param name="barcode_encoding" type="select" label="Barcode location">
-                    <expand macro="barcode_encoding_single" type="Barcode" />
-                </param>
-            </when>
-            <when value="paired">
-                <param name="fqinputs" type="data_collection" collection_type="list:paired" label="paired-end reads infile(s)" format="fastqsanger,fastqsanger.gz"/>
-                <param name="barcode_encoding" type="select" label="Barcode location">
-                    <expand macro="barcode_encoding_pair" type="Barcode" />
-                </param>
-            </when>
-        </conditional>
-        <param name="barcode" argument="-b" type="data"  format="tabular,txt" label="Barcode file" />
-    </xml>
-    <token name="@FASTQ_INPUT_PREPROC@"><![CDATA[
-    #for $input in $input_type.fqinputs:
-        #if $input_type.options_type_selector == "single"
-            #set $isfq=$input.is_of_type('fastqsanger')
-            #set $name=$clean_ext($input.element_identifier)
-        #else:
-            #set $isfq=$input.forward.is_of_type('fastqsanger')
-            ## TODO if https://github.com/galaxyproject/galaxy/pull/7031 is
-            ## backported use element_identifier consistently and fix release in <tool>?
-            #set $name=$clean_ext($input.name)
-        #end if
-    
-        #if $isfq:
-            #set $ext = "fastq"
-            #set inputype = "fastq"
-        #else
-            #set $ext = "fastq.gz"
-            #set inputype = "gzfastq"
-        #end if
-    
-        #if $input_type.options_type_selector == "single"
-            ln -s '$input' 'stacks_inputs/${name}.${ext}' &&
-        #else:
-            ## procrad needs _R[12]_ in the file name, so we add an add 0
-            ln -s '$input.forward' 'stacks_inputs/${name}_R1_0.${ext}' &&
-            ln -s '$input.reverse' 'stacks_inputs/${name}_R2_0.${ext}' &&
-        #end if
-    #end for
-    ]]></token>
+
     <token name="@PROCESS_IOOPTIONS@"><![CDATA[
     -p stacks_inputs/
-    #if $input_type.options_type_selector == "paired"
+    #if $input_type.input_type_select == "paired"
         --paired
     #end if
     -i $inputype
@@ -89,26 +39,26 @@
 
     <xml name="process_outputs">
         <collection name="demultiplexed" type="list" label="${tool.name} on ${on_string} Demultiplexed reads">
-            <filter>input_type['options_type_selector'] == "single"</filter>
+            <filter>input_type['input_type_select'] == "single"</filter>
             <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;name&gt;.+)" dir="stacks_outputs"/>
         </collection>
         <collection name="demultiplexed_paired" type="list:paired" label="${tool.name} on ${on_string} Demultiplexed reads">
-            <filter>input_type['options_type_selector'] == "paired"</filter>
+            <filter>input_type['input_type_select'] == "paired"</filter>
             <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs"/>
         </collection>
 
         <collection name="remaining" type="list:paired" label="${tool.name} on ${on_string} Remaining orphan reads">
-            <filter>input_type['options_type_selector'] == "paired"</filter>
+            <filter>input_type['input_type_select'] == "paired"</filter>
             <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.rem\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs/remaining"/>
         </collection>
 
         <!-- note irrespective of -y output is always named fastq and are never zipped -->
         <collection name="discarded" type="list" label="${tool.name} on ${on_string} Discarded reads">
-            <filter>capture is True and input_type['options_type_selector'] == "single"</filter>
+            <filter>capture is True and input_type['input_type_select'] == "single"</filter>
             <expand macro="discover_faq_output_macro" pattern="(?P&lt;name&gt;.*)" dir="stacks_outputs/discarded"/>
         </collection>
         <collection name="discarded_paired" type="list:paired" label="${tool.name} on ${on_string} Discarded reads">
-            <filter>capture is True and input_type['options_type_selector'] == "paired"</filter>
+            <filter>capture is True and input_type['input_type_select'] == "paired"</filter>
             <expand macro="discover_faq_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs/discarded"/>
         </collection>
     </xml>
@@ -116,7 +66,7 @@
     <!-- FASTQ filtering options -->
     <xml name="process_filter">
         <conditional name="filter_cond" >
-            <param name="filter_select" type="select" label="do quality filtering">
+            <param name="filter_select" type="select" label="Do quality filtering">
                 <option value="yes">Yes</option>
                 <option value="no" selected="true">No</option>
             </param>
@@ -125,10 +75,10 @@
                 <param name="score" type="integer" value="10" min="0" max="40" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded" />
                 <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" />
                 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/>
-                <param argument="--filter_illumina" type="boolean" checked="false" truevalue="--filter_illumina" falsevalue="" label="discard reads that have been marked by Illumina's chastity/purity filter as failing" />
+                <param argument="--filter_illumina" type="boolean" checked="false" truevalue="--filter_illumina" falsevalue="" label="Discard reads that have been marked by Illumina's chastity/purity filter as failing" />
             </when>
             <when value="no">
-                <param argument="--len_limit" type="integer" value="" optional="true" label="minimum sequence length" help="useful if your data has already been trimmed"/>
+                <param argument="--len_limit" type="integer" value="" optional="true" label="Minimum sequence length" help="useful if your data has already been trimmed"/>
             </when>
         </conditional>
         <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
@@ -153,7 +103,7 @@
         && mv stacks_outputs/*discards stacks_outputs/discarded/
 
         ## fix the _R[12]_0 that was added for preparing the input
-        #if $input_type.options_type_selector == 'paired':
+        #if $input_type.input_type_select == 'paired':
             && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/_R1_0/.1/; s/_R2_0/.2/;')"; done
         #end if
         ## also remove the gz which is added by procrad (but its uncompressed)
@@ -167,20 +117,18 @@
         #end if
     #end if
     ## prepare paired read output for processing in galaxy
-    #if $input_type.options_type_selector == 'paired':
+    #if $input_type.input_type_select == 'paired':
         && mkdir stacks_outputs/remaining
         && find stacks_outputs -iregex ".*\.rem\.[12]\.f[aq]\(\.gz\)?" | while read file; do mv "\$file" stacks_outputs/remaining/; done
         && find stacks_outputs/ -iregex ".*.f[aq]\(\.gz\)?" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.1\./.forward./; s/\.2\./.reverse./')"; done
     #end if
     ]]></token>
 
-
-
     <!-- adapter trimming options -->
     <xml name="process_adapter">
-            <param argument="--adapter_1" type="text" value="" optional="true" label="adaptor sequence that may occur on the first read" />
-            <param argument="--adapter_2" type="text" value="" optional="true" label="adaptor sequence that may occur on the paired-read" />
-            <param argument="--adapter_mm" type="integer" value="" optional="true" label="number of mismatches allowed in the adapter sequence"/>
+            <param argument="--adapter_1" type="text" value="" optional="true" label="Adaptor sequence that may occur on the first read" />
+            <param argument="--adapter_2" type="text" value="" optional="true" label="Adaptor sequence that may occur on the paired-read" />
+            <param argument="--adapter_mm" type="integer" value="" optional="true" label="Number of mismatches allowed in the adapter sequence"/>
     </xml>
     <token name="@PROCESS_ADAPTER@"><![CDATA[
     ## Adapter options
@@ -202,9 +150,9 @@
                 <option value="-r">yes</option>
                 <option value="" selected="true">no</option>
             </param>
-	    <when value="-r">
-                <param argument="--barcode_dist_1" type="integer" value="" optional="true" label="number of allowed mismatches when rescuing first read barcodes" help="(default 1)"/>
-    	        <param argument="--barcode_dist_2" type="integer" value="" optional="true" label="number of allowed mismatches when rescuing paired read barcodes" help="(default value for single end barcodes)"/>
+            <when value="-r">
+                <param argument="--barcode_dist_1" type="integer" value="" optional="true" label="Number of allowed mismatches when rescuing first read barcodes" help="(default 1)"/>
+                <param argument="--barcode_dist_2" type="integer" value="" optional="true" label="Number of allowed mismatches when rescuing paired read barcodes" help="(default value for single end barcodes)"/>
             </when>
             <when value=""/>
         </conditional>
@@ -221,7 +169,7 @@
     #end if
     ]]></token>
 
-    <!-- advanced options that are shared --> 
+    <!-- advanced options that are shared -->
     <xml name="common_advanced">
         <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" />
         <param argument="--retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" label="Retain unmodified FASTQ headers in the output" />