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diff plasmidspades.xml @ 0:eabeb1a74dac draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
author iuc
date Sun, 23 Jan 2022 21:32:59 +0000
parents
children 6aad515a5270
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plasmidspades.xml	Sun Jan 23 21:32:59 2022 +0000
@@ -0,0 +1,382 @@
+<tool id="spades_plasmidspades" name="plasmidSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+    <description>extract and assembly plasmids from WGS data</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[ 
+
+#set $library = 1
+
+@PREPROCESS_INPUT_FILES_MAIN@
+#if $additional_reads.selector == 'true'
+    @PREPROCESS_INPUT_FILES_ADDITIONAL@
+#end if
+@PREPROCESS_NANOPORE_PACBIO_FILES@
+@PREPROCESS_SANGER_FILES@
+@PREPROCESS_CONTIGS_FILES@
+@PREPROCESS_ASSEMBLY_GRAPH_FILES@
+
+## run
+plasmidspades.py
+    $operation_mode
+    -o 'output'
+    @RESOURCES@
+    @INPUT_READS_MAIN@
+    #if $additional_reads.selector == 'true'
+        @INPUT_READS_ADDITIONAL@
+    #end if
+    ## reads
+    @NANOPORE_PACBIO@
+    @SANGER@
+    @CONTIGS@
+    @ASSEMBLY_GRAPH@
+    ## parameter
+    --cov-cutoff $cov_cond.cov_cutoff
+    @KMER@
+    @PIPELINE_OPTIONS@
+    @PHREDOFFSET@
+    ## postprocessing
+    @STATS@
+    @CORRECTED@
+    ]]></command>
+    <inputs>
+        <expand macro="operation_mode"/>
+        <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)"/>
+        <section name="arf" title="Additional read files">
+            <expand macro="nanopore_pacbio"/>
+            <expand macro="sanger"/>
+            <expand macro="contigs"/>
+            <expand macro="assembly_graph"/>
+        </section>
+        <expand macro="pipeline_options">
+            <option value="--careful">Careful: tries to reduce the number of mismatches and short indels. Only recommended for small genomes (--careful)</option>
+            <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option>
+        </expand>
+        <expand macro="covcutoff"/>
+        <expand macro="kmer"/>
+        <expand macro="phred"/>
+        <expand macro="optional_output"/>
+    </inputs>
+    <outputs>
+        <expand macro="out_ag"/>
+        <expand macro="out_ags"/>
+        <expand macro="out_cn"/>
+        <expand macro="out_cp"/>
+        <expand macro="out_cr"/>
+        <expand macro="out_cs"/>
+        <expand macro="out_l"/>
+        <expand macro="out_sc"/>
+        <expand macro="out_sp"/>
+        <expand macro="out_ss"/>
+   </outputs>
+    <tests>
+        <!--
+        used in a test:
+            single library: 12, 1, 2
+            multiple libraries: s, pe#-12, pe#-1, pe#-2, pe#-<or>
+            k, phred-offset, disablerr, iontorrent, careful, only-assembler, only-error-correction
+
+        not used in a test:
+            single library: merged, s
+            multiple libraries: pe#-m, pe#-s, mp#-12, mp#-1, mp#-2, mp#-<or>, mp#-s, hqmp#-12, hqmp#-1, hqmp#-2, hqmp#-s, hqmp#-<or>, nxmate#-1, nxmate-#2
+            pacbio, nanopore, sanger, trusted-contigs, untrusted-contigs, tslr
+        -->
+
+        <!-- #1 single, separate, fastq.gz, default parameters -->
+         <test expect_num_outputs="4">
+            <conditional name="singlePaired">
+                <param name="sPaired" value="paired"/>
+                <param name="input1" value="pl1.fq.gz"/>
+                <param name="input2" value="pl2.fq.gz"/>
+            </conditional>
+            <output name="out_ag">
+                <assert_contents>
+                    <has_n_lines n="326"/>
+                    <has_text_matching expression=">EDGE_22_length_9689_cov_4.668331:EDGE_22_length_9689_cov_4.668331"/>
+                </assert_contents>
+            </output>
+            <output name="out_ags">
+                <assert_contents>
+                    <has_n_lines n="3"/>
+                    <has_text_matching expression="S.+"/>
+                </assert_contents>
+            </output>
+            <output name="out_cn">
+                <assert_contents>
+                    <has_n_lines n="163"/>
+                    <has_text_matching expression=">NODE\_1\_length\_9689\_cov\_.+"/>
+                </assert_contents>
+            </output>
+            <output name="out_sc">
+                <assert_contents>
+                    <has_n_lines n="163"/>
+                    <has_text_matching expression=">NODE\_1\_length\_9689.+"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #2 single, separate, fastq, all outputs and custom parameters -->
+        <test expect_num_outputs="10">
+            <conditional name="singlePaired">
+                <param name="sPaired" value="paired"/>
+                <param name="input1" value="pl1.fq.gz"/>
+                <param name="input2" value="pl2.fq.gz"/>
+            </conditional>
+            <conditional name="cov_cond">
+                <param name="cov_sel" value="auto"/>
+            </conditional>
+            <param name="phred_offset" value="33"/>
+            <param name="optional_output" value="ag,ags,cn,cp,cr,cs,l,sc,sp,ss"/>
+            <output name="out_ag">
+                <assert_contents>
+                    <has_n_lines n="326"/>
+                    <has_text_matching expression=">EDGE_.+"/>
+                </assert_contents>
+            </output>
+            <output name="out_ags">
+                <assert_contents>
+                    <has_n_lines n="3"/>
+                    <has_text_matching expression="S.+"/>
+                </assert_contents>
+            </output>
+            <output name="out_cn">
+                <assert_contents>
+                    <has_n_lines n="163"/>
+                    <has_text_matching expression=">NODE.+"/>
+                </assert_contents>
+            </output>
+            <output name="out_cp">
+                <assert_contents>
+                    <has_n_lines n="4"/>
+                </assert_contents>
+            </output>
+            <output name="out_cs">
+                <assert_contents>
+                    <has_n_lines n="1"/>
+                    <has_text_matching expression="#name&#009;length&#009;coverage"/>
+                </assert_contents>
+            </output>
+            <output_collection name="out_cr" type="list" count="3">
+                <element name="pl1.fq.gz.fastq.00.0_0.cor">
+                    <assert_contents>
+                        <has_size value="72173" delta="1000"/>
+                    </assert_contents>
+                </element>
+                <element name="pl2.fq.gz.fastq.00.0_0.cor">
+                    <assert_contents>
+                        <has_size value="72173" delta="1000"/>
+                    </assert_contents>
+                </element>
+                <element name="pl_unpaired.00.0_0.cor">
+                    <assert_contents>
+                        <has_size value="392" delta="100"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output name="out_l">
+                <assert_contents>
+                    <has_text_matching expression="Thank you for using SPAdes!"/>
+                </assert_contents>
+            </output>
+            <output name="out_sc">
+                <assert_contents>
+                    <has_n_lines n="163"/>
+                </assert_contents>
+            </output>
+            <output name="out_sp">
+                <assert_contents>
+                    <has_n_lines n="4"/>
+                </assert_contents>
+            </output>
+            <output name="out_ss">
+                <assert_contents>
+                    <has_n_lines n="1"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #3 multiple, single & paired-end, test dataset not valid -->
+        <test expect_num_outputs="1">
+            <param name="operation_mode" value="--only-assembler"/>
+            <conditional name="singlePaired">
+                <param name="sPaired" value="interlaced"/>
+                <param name="input1" value="ecoli_1K.fastq.gz"/>
+            </conditional>
+            <conditional name="additional_reads">
+                <param name="selector" value="true"/>
+                <conditional name="singlePaired">
+                    <param name="sPaired" value="paired"/>
+                    <param name="input1" value="pl1.fq.gz"/>
+                    <param name="input2" value="pl2.fq.gz"/>
+                </conditional>
+                <param name="type_paired" value="mp"/>
+                <param name="orientation" value="rf"/>
+            </conditional>
+            <param name="mode_sel" value="--careful"/>
+            <param name="optional_output" value="l"/>
+            <output name="out_l">
+                <assert_contents>
+                    <has_text_matching expression="Thank you for using SPAdes!"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #4 test dataset not valid-->
+        <test expect_num_outputs="1">
+            <conditional name="singlePaired">
+                <param name="sPaired" value="paired"/>
+                <param name="input1" value="pl1.fq.gz"/>
+                <param name="input2" value="pl2.fq.gz"/>
+            </conditional>
+            <param name="mode_sel" value="--careful"/>
+            <param name="optional_output" value="l"/>
+            <output name="out_l">
+                <assert_contents>
+                    <has_text_matching expression="Thank you for using SPAdes!"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #5 only corrected reads are created as an output -->
+        <test expect_num_outputs="2">
+            <param name="operation_mode" value="--only-error-correction"/>
+            <conditional name="singlePaired">
+                <param name="sPaired" value="paired"/>
+                <param name="input1" value="pl1.fq.gz"/>
+                <param name="input2" value="pl2.fq.gz"/>
+            </conditional>
+            <param name="optional_output" value="cr,l"/>
+            <output_collection name="out_cr" type="list" count="3">
+                <element name="pl1.fq.gz.fastq.00.0_0.cor">
+                    <assert_contents>
+                        <has_size value="72173" delta="1000"/>
+                    </assert_contents>
+                </element>
+                <element name="pl2.fq.gz.fastq.00.0_0.cor">
+                    <assert_contents>
+                        <has_size value="72173" delta="1000"/>
+                    </assert_contents>
+                </element>
+                <element name="pl_unpaired.00.0_0.cor">
+                    <assert_contents>
+                        <has_size value="392" delta="100"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output name="out_l">
+                <assert_contents>
+                    <has_text_matching expression="Thank you for using SPAdes!"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #6 only corrected reads are created as an output -->
+        <test expect_num_outputs="2">
+            <param name="operation_mode" value="--only-error-correction"/>
+            <conditional name="singlePaired">
+                <param name="sPaired" value="paired"/>
+                <param name="input1" value="pl1.fq.gz"/>
+                <param name="input2" value="pl2.fq.gz"/>
+            </conditional>
+            <param name="optional_output" value="cr,l"/>
+            <output_collection name="out_cr" type="list" count="3">
+                <element name="pl1.fq.gz.fastq.00.0_0.cor">
+                    <assert_contents>
+                        <has_size value="72173" delta="1000"/>
+                    </assert_contents>
+                </element>
+                <element name="pl2.fq.gz.fastq.00.0_0.cor">
+                    <assert_contents>
+                        <has_size value="72173" delta="1000"/>
+                    </assert_contents>
+                </element>
+                <element name="pl_unpaired.00.0_0.cor">
+                    <assert_contents>
+                        <has_size value="392" delta="100"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output name="out_l">
+                <assert_contents>
+                    <has_text_matching expression="Thank you for using SPAdes!"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #7 hybrid assembly: nanpopore, pacbio, sanger, untrustedcontigs -->
+        <test expect_num_outputs="2">
+            <conditional name="singlePaired">
+                <param name="sPaired" value="paired"/>
+                <param name="input1" value="pl1.fq.gz"/>
+                <param name="input2" value="pl2.fq.gz"/>
+            </conditional>
+            <section name="arf">
+                <param name="nanopore" value="ecoli_1K.fastq.gz"/>
+                <param name="pacbio" value="ecoli_1K.fastq.gz"/>
+                <param name="sanger" value="ecoli_1K.fastq.gz"/>
+                <param name="untrusted_contigs" value="ecoli_1K.fasta.gz"/>
+            </section>
+            <assert_command>
+                <has_text text="--nanopore"/>
+                <has_text text="--pacbio"/>
+                <has_text text="--sanger"/>
+                <has_text text="--untrusted-contigs"/>
+            </assert_command>
+            <param name="mode_sel" value="--careful"/>
+            <param name="optional_output" value="cr,l"/>
+            <output_collection name="out_cr" type="list" count="3">
+                <element name="pl1.fq.gz.fastq.00.0_0.cor">
+                    <assert_contents>
+                        <has_size value="72173" delta="1000"/>
+                    </assert_contents>
+                </element>
+                <element name="pl2.fq.gz.fastq.00.0_0.cor">
+                    <assert_contents>
+                        <has_size value="72173" delta="1000"/>
+                    </assert_contents>
+                </element>
+                <element name="pl_unpaired.00.0_0.cor">
+                    <assert_contents>
+                        <has_size value="392" delta="100"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output name="out_l">
+                <assert_contents>
+                    <has_text_matching expression="Thank you for using SPAdes!"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+@HELP_WID@
+
+plasmidSPAdes is a subtool for assembling plasmid data sets.
+
+**Input**
+
+@HELP_IN@
+
+**Output**
+
+@HELP_OUT_AG@
+@HELP_OUT_AGS@
+@HELP_OUT_C@
+@HELP_OUT_CP@
+@HELP_OUT_CR@
+@HELP_OUT_CS@
+@HELP_OUT_L@
+@HELP_OUT_S@
+@HELP_OUT_SP@
+@HELP_OUT_SS@
+
+**References**
+
+More information can be found on `github <https://github.com/ablab/spades>`_  and on the `project website <http://cab.spbu.ru/software/plasmid-spades>`_.
+    ]]></help>
+    <expand macro="citations">
+        <citation type="doi">10.1093/bioinformatics/btw493</citation>
+    </expand>
+</tool>