diff prinseq.xml @ 5:1ee282794de3 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 34e8262534e22f0d391a81b06374744c4af8da24"

--- a/prinseq.xml	Wed Jul 07 09:22:27 2021 +0000
+++ b/prinseq.xml	Sun Mar 20 10:51:09 2022 +0000
@@ -1,5 +1,8 @@
-<tool id="prinseq" name="PRINSEQ" version="@TOOL_VERSION+galaxy1">
+<tool id="prinseq" name="PRINSEQ" version="@TOOL_VERSION+galaxy2" profile="20.05">
     <description>to process quality of sequences</description>
+    <xrefs>
+        <xref type="bio.tools">prinseq</xref>
+    </xrefs>
     <macros>
         <token name="@TOOL_VERSION">0.20.4</token>
     </macros>
@@ -8,7 +11,6 @@
     </requirements>
 
     <stdio>
-        <exit_code range="1:"   level="fatal"   description="" />
         <regex match="ERROR"
                source="stderr"
                level="fatal"
@@ -25,36 +27,57 @@
 ]]>
     </version_command>
 
-    <command>
+    <command detect_errors="exit_code">
 <![CDATA[
-        mkdir tmp/
+        mkdir tmp/ &&
+
+        #if $seq_type.seq_type_opt == "single"
+            #set fwd = $seq_type.input_singles
+            #set rev = None
+        #else if $seq_type.seq_type_opt == "paired"
+            #set fwd = $seq_type.input_mate1
+            #set rev = $seq_type.input_mate2
+        #else
+            #set fwd = $seq_type.input_collection.forward
+            #set rev = $seq_type.input_collection.reverse
+        #end if
 
-        &&
+        #if $rev and $fwd.ext != $rev.ext:
+            >&2 echo 'Both pairs from your paired-end library need to be from the same filetype.' &&
+            exit 1;
+        #end if
+        
+        #if $fwd.ext.endswith(".gz")
+            gunzip -c '$fwd' > fwd.fastq &&
+        #else
+            ln -s '$fwd' fwd.fastq &&
+        #end if
+        
+        #if $rev
+            #if $rev.ext.endswith(".gz")
+                gunzip -c '$rev' > rev.fastq &&
+            #else
+                ln -s '$rev' rev.fastq &&
+            #end if
+        #end if
+
+        ## create empty output files
+        #if $seq_type.seq_type_opt == "single"
+            touch tmp/good_sequences.fastq tmp/rejected_sequences.fastq &&
+        #else
+            touch tmp/good_sequences_1.fastq tmp/good_sequences_1_singletons.fastq tmp/rejected_sequences_1.fastq &&
+            touch tmp/good_sequences_2.fastq tmp/good_sequences_2_singletons.fastq tmp/rejected_sequences_2.fastq &&
+        #end if
+
 
         prinseq-lite.pl
-            #if $seq_type.seq_type_opt == "single":
-                -fastq '$seq_type.input_singles'
-                #if $seq_type.input_singles.is_of_type('fastqillumina'):
-                    -phred64
-                #end if
-            #elif $seq_type.seq_type_opt == "paired":
-                -fastq '$seq_type.input_mate1'
-                -fastq2 '$seq_type.input_mate2'
-                #if $seq_type.input_mate1.ext != $seq_type.input_mate2.ext:
-                    #import sys
-                    #silent sys.stderr.write( 'Both pairs from your paired-end library need to be from the same filetype.' )
-                #end if
-                #if $seq_type.input_mate1.is_of_type('fastqillumina'):
-                    -phred64
-                #end if
-            #else 
-                -fastq '$seq_type.input_collection.forward'
-                -fastq2 '$seq_type.input_collection.reverse'
-                #if $seq_type.input_collection.forward.is_of_type('fastqillumina'):
-                    -phred64
-                #end if
+            -fastq fwd.fastq
+            #if $rev
+                -fastq2 rev.fastq
             #end if
-
+            #if $fwd.ext.startswith('fastqillumina'):
+                -phred64
+            #end if
             -out_good "tmp/good_sequences"
             -out_bad "tmp/rejected_sequences"
 
@@ -226,9 +249,16 @@
 
         prinseq-graphs-noPCA.pl -i "tmp/stats.gd" -html_all -o stats_html
         *#
+
+        #if $fwd.ext.endswith('.gz')
+            && for f in tmp/*.fastq;
+            do
+                gzip -c \$f > tmp_file &&
+                mv tmp_file \$f;
+            done
+        #end if
 ]]>
     </command>
-
     <inputs>
         <conditional name="seq_type">
             <param name="seq_type_opt" type="select" label="Is this library paired- or single-end?">
@@ -237,11 +267,11 @@
               <option value="paired_collection">Paired Collection</option>
             </param>
             <when value="single">
-                <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
+                <param name="input_singles" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz" label="FASTQ file" help="FASTQ files." />
             </when>
             <when value="paired">
-                <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
-                <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
+                <param name="input_mate1" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz" label="FASTQ file" help="FASTQ files." />
+                <param name="input_mate2" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz" label="FASTQ file" help="FASTQ files." />
             </when>
             <when value="paired_collection">
                 <param name="input_collection" type="data_collection" collection_type="paired" label="FASTQ collection" help="FASTQ data in a paired collection" />
@@ -630,49 +660,55 @@
     </inputs>
 
     <outputs>
-        <data format_source="input_singles" name="good_sequence_file" from_work_dir="tmp/good_sequences.fastq"
+        <data name="good_sequence_file" format_source="input_singles" from_work_dir="tmp/good_sequences.fastq"
             label="${tool.name} on ${on_string}: Good sequences" >
             <filter>seq_type['seq_type_opt'] == "single"</filter>
         </data>
-        <data format_source="input_singles" name="rejected_sequence_file" from_work_dir="tmp/rejected_sequences.fastq"
+        <data name="rejected_sequence_file" format_source="input_singles" from_work_dir="tmp/rejected_sequences.fastq"
             label="${tool.name} on ${on_string}: Rejected sequences" >
             <filter>seq_type['seq_type_opt'] == "single"</filter>
         </data>
 
-        <data format_source="input_mate1" name="good_sequences_1_file" from_work_dir="tmp/good_sequences_1.fastq"
+        <data name="good_sequences_1_file" format_source="input_mate1" from_work_dir="tmp/good_sequences_1.fastq"
             label="${tool.name} on ${on_string}: Good sequences for R1" >
             <filter>seq_type['seq_type_opt'] == "paired"</filter>
         </data>
-        <data format_source="input_mate1" name="good_sequences_1_singletons_file" from_work_dir="tmp/good_sequences_1_singletons.fastq"
+        <data name="good_sequences_1_singletons_file" format_source="input_mate1" from_work_dir="tmp/good_sequences_1_singletons.fastq"
             label="${tool.name} on ${on_string}: Good singleton sequences for R1" >
             <filter>seq_type['seq_type_opt'] == "paired"</filter>
         </data>
-        <data format_source="input_mate1" name="rejected_sequence_1_file" from_work_dir="tmp/rejected_sequences_1.fastq"
+        <data name="rejected_sequence_1_file" format_source="input_mate1" from_work_dir="tmp/rejected_sequences_1.fastq"
             label="${tool.name} on ${on_string}: Rejected sequences for R1" >
             <filter>seq_type['seq_type_opt'] == "paired"</filter>
         </data>
-        <data format_source="input_mate2" name="good_sequences_2_file" from_work_dir="tmp/good_sequences_2.fastq"
+        <data name="good_sequences_2_file" format_source="input_mate2" from_work_dir="tmp/good_sequences_2.fastq"
             label="${tool.name} on ${on_string}: Good sequences for R2" >
             <filter>seq_type['seq_type_opt'] == "paired"</filter>
         </data>
-        <data format_source="input_mate2" name="good_sequences_2_singletons_file" from_work_dir="tmp/good_sequences_2_singletons.fastq"
+        <data name="good_sequences_2_singletons_file" format_source="input_mate2" from_work_dir="tmp/good_sequences_2_singletons.fastq"
             label="${tool.name} on ${on_string}: Good singleton sequences for R2" >
             <filter>seq_type['seq_type_opt'] == "paired"</filter>
         </data>
-        <data format_source="input_mate2" name="rejected_sequence_2_file" from_work_dir="tmp/rejected_sequences_2.fastq"
+        <data name="rejected_sequence_2_file" format_source="input_mate2" from_work_dir="tmp/rejected_sequences_2.fastq"
             label="${tool.name} on ${on_string}: Rejected sequences for R2" >
             <filter>seq_type['seq_type_opt'] == "paired"</filter>
         </data>
 
-        <collection name="good_sequences_collection" type="paired">
+        <collection name="good_sequences_collection" format_source="input_collection" type="paired">
+            <data name="forward" from_work_dir="tmp/good_sequences_1.fastq"/>
+            <data name="reverse" from_work_dir="tmp/good_sequences_2.fastq"/>
             <filter>seq_type['seq_type_opt'] == "paired_collection"</filter>
         </collection>
 
-        <collection name="singletons_collection" type="paired">
+        <collection name="singletons_collection" format_source="input_collection" type="paired">
+            <data name="forward" from_work_dir="tmp/good_sequences_1_singletons.fastq"/>
+            <data name="reverse" from_work_dir="tmp/good_sequences_2_singletons.fastq"/>
             <filter>seq_type['seq_type_opt'] == "paired_collection"</filter>
         </collection>
 
-        <collection name="rejected_sequences_collection" type="paired">
+        <collection name="rejected_sequences_collection" format_source="input_collection" type="paired">
+            <data name="forward" from_work_dir="tmp/rejected_sequences_1.fastq"/>
+            <data name="reverse" from_work_dir="tmp/rejected_sequences_2.fastq"/>
             <filter>seq_type['seq_type_opt'] == "paired_collection"</filter>
         </collection>
 
@@ -681,9 +717,9 @@
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name='seq_type_opt' value="single"/>
-            <param name="input_singles" value="prinseq_input_sequences.fastq" ftype="fastqsanger"/>
+            <param name="input_singles" value="prinseq_input_sequences.fastq.gz" ftype="fastqsanger.gz"/>
             <param name='apply_filter_treatments' value="true"/>
             <param name='apply_length_filter_treatments' value="true"/>
             <param name='apply_min_length_filter_treatments' value="true"/>
@@ -715,8 +751,158 @@
             <param name="rule_quality_trimming_treatments" value="lt" />
             <param name="window_quality_trimming_treatments" value="1"/>
             <param name="step_quality_trimming_treatments" value="1"/>
-
-            <output name="good_sequence_file" file="prinseq_good_sequences.fastq" ftype="fastqsanger"/>
+            <output name="good_sequence_file" ftype="fastqsanger.gz">
+                <assert_contents>
+                    <has_size value="11219" delta="1000"/>
+                </assert_contents>
+            </output>
+            <output name="rejected_sequence_file" ftype="fastqsanger.gz">
+                <assert_contents>
+                    <has_size value="14208" delta="1000"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="6">
+            <param name='seq_type_opt' value="paired"/>
+            <param name="input_mate1" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq" ftype="fastqsanger"/>
+            <param name="input_mate2" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R2.fastq" ftype="fastqsanger"/>
+            <param name='apply_filter_treatments' value="true"/>
+            <param name='apply_length_filter_treatments' value="true"/>
+            <param name='apply_min_length_filter_treatments' value="true"/>
+            <param name="min_length_filter_treatment_value" value="50"/>
+            <param name='apply_max_length_filter_treatments' value="false" />
+            <param name='apply_quality_filter_treatments' value="true"/>
+            <param name='apply_min_quality_filter_treatments' value="false" />
+            <param name='apply_max_quality_filter_treatments' value="false"/>
+            <param name='apply_mean_quality_filter_treatments' value="true"/>
+            <param name='apply_min_mean_quality_filter_treatments' value="true"/>
+            <param name="min_mean_quality_filter_treatment_value" value="15"/>
+            <param name='apply_max_mean_quality_filter_treatments' value="false"/>
+            <param name='apply_base_content_filter_treatments' value="true"/>
+            <param name='apply_GC_perc_content_filter_treatments' value="false"/>
+            <param name='apply_N_number_content_filter_treatments' value="false"/>
+            <param name='apply_N_percentage_content_filter_treatments' value="true"/>
+            <param name="N_percentage_content_filter_treatment_value" value="2"/>
+            <param name='apply_other_base_content_filter_treatments' value="false"/>
+            <param name='apply_complexity_filter_treatments' value="false"/>
+            <param name='apply_trimming_treatments' value="true" />
+            <param name='apply_length_trimming_treatments' value="false"/>
+            <param name='apply_position_trimming_treatments' value="false"/>
+            <param name='apply_tail_trimming_treatments' value="false"/>
+            <param name='apply_quality_trimming_treatments' value="true"/>
+            <param name='apply_left_quality_trimming_treatments' value="false"/>
+            <param name='apply_right_quality_trimming_treatments' value="true" />
+            <param name="right_quality_trimming_treatment_value" value="20"/>
+            <param name="type_quality_trimming_treatments" value="min"/>
+            <param name="rule_quality_trimming_treatments" value="lt" />
+            <param name="window_quality_trimming_treatments" value="1"/>
+            <param name="step_quality_trimming_treatments" value="1"/>
+            <output name="good_sequences_1_file" ftype="fastqsanger">
+                <assert_contents>
+                    <has_n_lines n="36"/>
+                </assert_contents>
+            </output>
+            <output name="good_sequences_1_singletons_file" ftype="fastqsanger">
+                <assert_contents>
+                    <has_n_lines n="44"/>
+                </assert_contents>
+            </output>
+            <output name="rejected_sequence_1_file" ftype="fastqsanger">
+                <assert_contents>
+                    <has_n_lines n="0"/>
+                </assert_contents>
+            </output>
+            <output name="good_sequences_2_file" ftype="fastqsanger">
+                <assert_contents>
+                    <has_n_lines n="36"/>
+                </assert_contents>
+            </output>
+            <output name="good_sequences_2_singletons_file" ftype="fastqsanger">
+                <assert_contents>
+                    <has_n_lines n="8"/>
+                </assert_contents>
+            </output>
+            <output name="rejected_sequence_2_file" ftype="fastqsanger">
+                <assert_contents>
+                    <has_n_lines n="36"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="9">
+            <param name='seq_type_opt' value="paired_collection"/>
+            <param name="input_collection">
+                <collection type="paired">
+                    <element name="forward" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq.gz" ftype="fastqsanger.gz"/>
+                    <element name="reverse" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R2.fastq.gz" ftype="fastqsanger.gz"/>
+                </collection>
+            </param>
+            <param name='apply_filter_treatments' value="true"/>
+            <param name='apply_length_filter_treatments' value="true"/>
+            <param name='apply_min_length_filter_treatments' value="true"/>
+            <param name="min_length_filter_treatment_value" value="50"/>
+            <param name='apply_max_length_filter_treatments' value="false" />
+            <param name='apply_quality_filter_treatments' value="true"/>
+            <param name='apply_min_quality_filter_treatments' value="false" />
+            <param name='apply_max_quality_filter_treatments' value="false"/>
+            <param name='apply_mean_quality_filter_treatments' value="true"/>
+            <param name='apply_min_mean_quality_filter_treatments' value="true"/>
+            <param name="min_mean_quality_filter_treatment_value" value="15"/>
+            <param name='apply_max_mean_quality_filter_treatments' value="false"/>
+            <param name='apply_base_content_filter_treatments' value="true"/>
+            <param name='apply_GC_perc_content_filter_treatments' value="false"/>
+            <param name='apply_N_number_content_filter_treatments' value="false"/>
+            <param name='apply_N_percentage_content_filter_treatments' value="true"/>
+            <param name="N_percentage_content_filter_treatment_value" value="2"/>
+            <param name='apply_other_base_content_filter_treatments' value="false"/>
+            <param name='apply_complexity_filter_treatments' value="false"/>
+            <param name='apply_trimming_treatments' value="true" />
+            <param name='apply_length_trimming_treatments' value="false"/>
+            <param name='apply_position_trimming_treatments' value="false"/>
+            <param name='apply_tail_trimming_treatments' value="false"/>
+            <param name='apply_quality_trimming_treatments' value="true"/>
+            <param name='apply_left_quality_trimming_treatments' value="false"/>
+            <param name='apply_right_quality_trimming_treatments' value="true" />
+            <param name="right_quality_trimming_treatment_value" value="20"/>
+            <param name="type_quality_trimming_treatments" value="min"/>
+            <param name="rule_quality_trimming_treatments" value="lt" />
+            <param name="window_quality_trimming_treatments" value="1"/>
+            <param name="step_quality_trimming_treatments" value="1"/>
+            <output_collection name="good_sequences_collection" type="paired">
+                <element name="forward" ftype="fastqsanger.gz">
+                    <assert_contents>
+                        <has_size value="605" delta="100"/>
+                    </assert_contents>
+                </element>
+                <element name="reverse" ftype="fastqsanger.gz">
+                    <assert_contents>
+                        <has_size value="667" delta="100"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="singletons_collection" type="paired">
+                <element name="forward" ftype="fastqsanger.gz">
+                    <assert_contents>
+                        <has_size value="720" delta="100"/>
+                    </assert_contents>
+                </element>
+                <element name="reverse" ftype="fastqsanger.gz">
+                    <assert_contents>
+                        <has_size value="219" delta="100"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="rejected_sequences_collection" type="paired">
+                <element name="forward" ftype="fastqsanger.gz">
+                    <assert_contents>
+                        <has_size value="0" delta="0"/>
+                    </assert_contents>
+                </element>
+                <element name="reverse" ftype="fastqsanger.gz">
+                    <assert_contents>
+                        <has_size value="718" delta="100"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
         </test>
     </tests>