Mercurial > repos > nml > spades

diff spades.xml @ 26:b512435320e3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
author iuc
date Wed, 12 Mar 2025 21:46:56 +0000
parents d5887ace0dd4
children
line wrap: on
line diff
--- a/spades.xml	Mon Mar 03 11:06:57 2025 +0000
+++ b/spades.xml	Wed Mar 12 21:46:56 2025 +0000
@@ -47,18 +47,17 @@
 
     ## postprocessing
     @STATS@
-    @CORRECTED@
     ]]></command>
     <inputs>
         <expand macro="operation_mode" help="To run read error correction, reads should be in FASTQ format."/>
-        <expand macro="input_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)"/>
-        <expand macro="input_additional_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)"/>
+        <expand macro="input_files_all" format="@INTYPES@" label="FASTA/FASTQ file(s)"/>
+        <expand macro="input_additional_files_all" format="@INTYPES@" label="FASTA/FASTQ file(s)"/>
         <section name="arf" title="Additional read files">
             <expand macro="nanopore_pacbio"/>
             <expand macro="sanger"/>
             <expand macro="contigs"/>
         </section>
-        <expand macro="pipeline_options">
+        <expand macro="pipeline_options" additional_help="&quot;Isolate&quot; is not compatible with &quot;Careful&quot; and Operation mode &quot;Only error correction&quot;">
             <option value="--sc">Single cell mode: required for MDA (single-cell) data (--sc)</option>
             <option value="--isolate">Isolate: highly recommended for high-coverage isolate and multi-cell data (--isolate)</option>
             <option value="--careful">Careful: ties to reduce the number of mismatches and short indels. Only recommended for small genomes (--careful)</option>
@@ -106,8 +105,10 @@
             </output>
             <output name="out_ags">
                 <assert_contents>
-                    <has_n_lines n="2"/>
+                    <has_n_lines n="3"/>
+                    <has_text_matching expression="H.+"/>
                     <has_text_matching expression="S.+"/>
+                    <has_text_matching expression="P.+"/>
                 </assert_contents>
             </output>
             <output name="out_cn">
@@ -126,9 +127,17 @@
         <!-- #2 single, separate, fastq, custom parameters  -->
         <test expect_num_outputs="9">
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired"/>
-                <param name="input1" value="ecoli_1K_1.fastq.gz"/>
-                <param name="input2" value="ecoli_1K_2.fastq.gz"/>
+                <param name="sPaired" value="paired_collection"/>
+                <param name="input">
+                    <collection type="list:paired">
+                        <element name="ecoli_1K">
+                            <collection type="paired">
+                                <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
+                                <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
+                            </collection>
+                        </element>
+                    </collection>
+                </param>
             </conditional>
             <param name="mode_sel" value="--isolate,--disable-rr,--iontorrent"/>
             <conditional name="cov_cond">
@@ -148,7 +157,8 @@
             </output>
             <output name="out_ags">
                 <assert_contents>
-                    <has_n_lines n="1"/>
+                    <has_n_lines n="2"/>
+                    <has_text_matching expression="H.+"/>
                     <has_text_matching expression="S.+"/>
                 </assert_contents>
             </output>
@@ -195,9 +205,17 @@
         <test expect_num_outputs="4">
             <param name="operation_mode" value="--only-assembler"/>
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired"/>
-                <param name="input1" value="ecoli_1K_1.fastq.gz"/>
-                <param name="input2" value="ecoli_1K_2.fastq.gz"/>
+                <param name="sPaired" value="paired_collection"/>
+                <param name="input">
+                    <collection type="list:paired">
+                        <element name="ecoli_1K">
+                            <collection type="paired">
+                                <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
+                                <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
+                            </collection>
+                        </element>
+                    </collection>
+                </param>
             </conditional>
             <output name="out_ag">
                 <assert_contents>
@@ -207,8 +225,10 @@
             </output>
             <output name="out_ags">
                 <assert_contents>
-                    <has_n_lines n="2"/>
+                    <has_n_lines n="3"/>
+                    <has_text_matching expression="H.+"/>
                     <has_text_matching expression="S.+"/>
+                    <has_text_matching expression="P.+"/>
                 </assert_contents>
             </output>
             <output name="out_cn">
@@ -233,9 +253,17 @@
             <conditional name="additional_reads">
                 <param name="selector" value="true"/>
                 <conditional name="singlePaired">
-                    <param name="sPaired" value="paired"/>
-                    <param name="input1" value="ecoli_1K_1.fastq.gz"/>
-                    <param name="input2" value="ecoli_1K_2.fastq.gz"/>
+                    <param name="sPaired" value="paired_collection"/>
+                    <param name="input">
+                        <collection type="list:paired">
+                            <element name="ecoli_1K">
+                                <collection type="paired">
+                                    <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
+                                    <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
+                                </collection>
+                            </element>
+                        </collection>
+                    </param>
                 </conditional>
             </conditional>
             <param name="mode_sel" value="--careful"/>
@@ -247,8 +275,10 @@
             </output>
             <output name="out_ags">
                 <assert_contents>
-                    <has_n_lines n="2"/>
+                    <has_n_lines n="3"/>
+                    <has_text_matching expression="H.+"/>
                     <has_text_matching expression="S.+"/>
+                    <has_text_matching expression="P.+"/>
                 </assert_contents>
             </output>
             <output name="out_cn">
@@ -274,9 +304,17 @@
             <conditional name="additional_reads">
                 <param name="selector" value="true"/>
                 <conditional name="singlePaired">
-                    <param name="sPaired" value="paired"/>
-                    <param name="input1" value="ecoli_1K_1.fastq.gz"/>
-                    <param name="input2" value="ecoli_1K_2.fastq.gz"/>
+                    <param name="sPaired" value="paired_collection"/>
+                    <param name="input">
+                        <collection type="list:paired">
+                            <element name="ecoli_1K">
+                                <collection type="paired">
+                                    <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
+                                    <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
+                                </collection>
+                            </element>
+                        </collection>
+                    </param>
                 </conditional>
             </conditional>
             <param name="mode_sel" value="--careful"/>
@@ -288,8 +326,10 @@
             </output>
             <output name="out_ags">
                 <assert_contents>
-                    <has_n_lines n="2"/>
+                    <has_n_lines n="3"/>
+                    <has_text_matching expression="H.+"/>
                     <has_text_matching expression="S.+"/>
+                    <has_text_matching expression="P.+"/>
                 </assert_contents>
             </output>
             <output name="out_cn">
@@ -315,17 +355,17 @@
             <param name="mode_sel" value="--careful"/>
             <param name="optional_output" value="cr,l"/>
             <output_collection name="out_cr" type="list" count="3">
-                <element name="ecoli_1K.fastq.gz_1.00.0_0">
+                <element name="ecoli_1K.fastq.gz_100.0_0">
                     <assert_contents>
-                        <has_size value="130317" delta="5000"/>
+                        <has_size value="130317" delta="7000"/>
                     </assert_contents>
                 </element>
-                <element name="ecoli_1K.fastq.gz_2.00.0_0">
+                <element name="ecoli_1K.fastq.gz_200.0_0">
                     <assert_contents>
-                        <has_size value="130317" delta="5000"/>
+                        <has_size value="130317" delta="7000"/>
                     </assert_contents>
                 </element>
-                <element name="ecoli_1K.fastq.gz__unpaired.00.0_0">
+                <element name="ecoli_1K.fastq.gz__unpaired00.0_0">
                     <assert_contents>
                         <has_size value="20" delta="5"/>
                     </assert_contents>
@@ -347,17 +387,17 @@
             <param name="mode_sel" value="--careful,--sc"/>
             <param name="optional_output" value="cr,l"/>
             <output_collection name="out_cr" type="list" count="3">
-                <element name="ecoli_1K.fastq.gz_1.00.0_0">
+                <element name="ecoli_1K.fastq.gz_100.0_0">
                     <assert_contents>
-                        <has_size value="130317" delta="5000"/>
+                        <has_size value="130317" delta="7000"/>
                     </assert_contents>
                 </element>
-                <element name="ecoli_1K.fastq.gz_2.00.0_0">
+                <element name="ecoli_1K.fastq.gz_200.0_0">
                     <assert_contents>
-                        <has_size value="130317" delta="5000"/>
+                        <has_size value="130317" delta="7000"/>
                     </assert_contents>
                 </element>
-                <element name="ecoli_1K.fastq.gz__unpaired.00.0_0">
+                <element name="ecoli_1K.fastq.gz__unpaired00.0_0">
                     <assert_contents>
                         <has_size value="20" delta="5"/>
                     </assert_contents>
@@ -380,13 +420,15 @@
             <output name="out_ag">
                 <assert_contents>
                     <has_n_lines n="36"/>
-                    <has_text_matching expression=">EDGE_7_length_1000_cov_140.639153"/>
+                    <has_text_matching expression=">EDGE_[0-9]+_length_[0-9]+_cov_[0-9]+\.[0-9]+"/>
                 </assert_contents>
             </output>
             <output name="out_ags">
                 <assert_contents>
-                    <has_n_lines n="2"/>
+                    <has_n_lines n="3"/>
+                    <has_text_matching expression="H.+"/>
                     <has_text_matching expression="S.+"/>
+                    <has_text_matching expression="P.+"/>
                 </assert_contents>
             </output>
             <output name="out_cn">
@@ -411,17 +453,17 @@
             </conditional>
             <param name="optional_output" value="cr,l"/>
             <output_collection name="out_cr" type="list" count="3">
-                <element name="ecoli_1K.fastq.gz_1.00.0_0">
+                <element name="ecoli_1K.fastq.gz_100.0_0">
                     <assert_contents>
-                        <has_size value="130317" delta="5000"/>
+                        <has_size value="130317" delta="7000"/>
                     </assert_contents>
                 </element>
-                <element name="ecoli_1K.fastq.gz_2.00.0_0">
+                <element name="ecoli_1K.fastq.gz_200.0_0">
                     <assert_contents>
-                        <has_size value="130317" delta="5000"/>
+                        <has_size value="130317" delta="7000"/>
                     </assert_contents>
                 </element>
-                <element name="ecoli_1K.fastq.gz__unpaired.00.0_0">
+                <element name="ecoli_1K.fastq.gz__unpaired00.0_0">
                     <assert_contents>
                         <has_size value="20" delta="5"/>
                     </assert_contents>
@@ -443,17 +485,17 @@
             <param name="mode_sel" value="--sc"/>
             <param name="optional_output" value="cr,l"/>
             <output_collection name="out_cr" type="list" count="3">
-                <element name="ecoli_1K.fastq.gz_1.00.0_0">
+                <element name="ecoli_1K.fastq.gz_100.0_0">
                     <assert_contents>
-                        <has_size value="130317" delta="5000"/>
+                        <has_size value="130317" delta="7000"/>
                     </assert_contents>
                 </element>
-                <element name="ecoli_1K.fastq.gz_2.00.0_0">
+                <element name="ecoli_1K.fastq.gz_200.0_0">
                     <assert_contents>
-                        <has_size value="130317" delta="5000"/>
+                        <has_size value="130317" delta="7000"/>
                     </assert_contents>
                 </element>
-                <element name="ecoli_1K.fastq.gz__unpaired.00.0_0">
+                <element name="ecoli_1K.fastq.gz__unpaired00.0_0">
                     <assert_contents>
                         <has_size value="20" delta="5"/>
                     </assert_contents>
@@ -480,8 +522,10 @@
             </output>
             <output name="out_ags">
                 <assert_contents>
-                    <has_n_lines n="2"/>
+                    <has_n_lines n="3"/>
+                    <has_text_matching expression="H.+"/>
                     <has_text_matching expression="S.+"/>
+                    <has_text_matching expression="P.+"/>
                 </assert_contents>
             </output>
             <output name="out_cn">
@@ -500,9 +544,17 @@
         <!-- #12 -->
         <test expect_num_outputs="4">
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired"/>
-                <param name="input1" value="ecoli_1K_1.fastq.gz"/>
-                <param name="input2" value="ecoli_1K_2.fastq.gz"/>
+                <param name="sPaired" value="paired_collection"/>
+                <param name="input">
+                    <collection type="list:paired">
+                        <element name="ecoli_1K">
+                            <collection type="paired">
+                                <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
+                                <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
+                            </collection>
+                        </element>
+                    </collection>
+                </param>
             </conditional>
             <param name="mode_sel" value="--sc,--careful"/>
             <output name="out_ag">
@@ -513,8 +565,10 @@
             </output>
             <output name="out_ags">
                 <assert_contents>
-                    <has_n_lines n="2"/>
+                    <has_n_lines n="3"/>
+                    <has_text_matching expression="H.+"/>
                     <has_text_matching expression="S.+"/>
+                    <has_text_matching expression="P.+"/>
                 </assert_contents>
             </output>
             <output name="out_cn">
@@ -534,9 +588,17 @@
         <test expect_num_outputs="4">
             <param name="operation_mode" value="--only-assembler"/>
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired"/>
-                <param name="input1" value="ecoli_1K_1.fastq.gz"/>
-                <param name="input2" value="ecoli_1K_2.fastq.gz"/>
+                <param name="sPaired" value="paired_collection"/>
+                <param name="input">
+                    <collection type="list:paired">
+                        <element name="ecoli_1K">
+                            <collection type="paired">
+                                <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
+                                <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
+                            </collection>
+                        </element>
+                    </collection>
+                </param>
             </conditional>
             <param name="mode_sel" value="--sc,--careful"/>
             <output name="out_ag">
@@ -547,8 +609,10 @@
             </output>
             <output name="out_ags">
                 <assert_contents>
-                    <has_n_lines n="2"/>
+                    <has_n_lines n="3"/>
+                    <has_text_matching expression="H.+"/>
                     <has_text_matching expression="S.+"/>
+                    <has_text_matching expression="P.+"/>
                 </assert_contents>
             </output>
             <output name="out_cn">
@@ -590,8 +654,10 @@
             </output>
             <output name="out_ags">
                 <assert_contents>
-                    <has_n_lines n="2"/>
+                    <has_n_lines n="3"/>
+                    <has_text_matching expression="H.+"/>
                     <has_text_matching expression="S.+"/>
+                    <has_text_matching expression="P.+"/>
                 </assert_contents>
             </output>
             <output name="out_cn">
@@ -610,9 +676,17 @@
         <!-- #15 mate-pair reads orientation rf-->
         <test expect_num_outputs="4">
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired"/>
-                <param name="input1" value="ecoli_1K_1.fastq.gz"/>
-                <param name="input2" value="ecoli_1K_2.fastq.gz"/>
+                <param name="sPaired" value="paired_collection"/>
+                <param name="input">
+                    <collection type="list:paired">
+                        <element name="ecoli_1K">
+                            <collection type="paired">
+                                <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/>
+                                <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/>
+                            </collection>
+                        </element>
+                    </collection>
+                </param>
                 <param name="type_paired" value="hqmp"/>
                 <param name="orientation" value="rf"/>
             </conditional>
@@ -624,7 +698,9 @@
             </output>
             <output name="out_ags">
                 <assert_contents>
-                    <has_n_lines n="1"/>
+                    <has_n_lines n="2"/>
+                    <has_text_matching expression="H.+"/>
+                    <has_text_matching expression="S.+"/>
                 </assert_contents>
             </output>
             <output name="out_cn">
@@ -663,8 +739,10 @@
             </output>
             <output name="out_ags">
                 <assert_contents>
-                    <has_n_lines n="2"/>
+                    <has_n_lines n="3"/>
+                    <has_text_matching expression="H.+"/>
                     <has_text_matching expression="S.+"/>
+                    <has_text_matching expression="P.+"/>
                 </assert_contents>
             </output>
             <output name="out_cn">