diff salmonquant.xml @ 10:4de6e2e40c7a draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/salmonquant.xml	Mon Sep 09 11:11:22 2019 -0400
@@ -0,0 +1,267 @@
+<tool id="salmon" name="Salmon quant" version="@VERSION@">
+    <description>Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+        #if $quant_type.qtype == "reads":
+            @indexing@
+            @salreads@
+        #else:
+            @salalign@
+        #end if
+        @salquant@
+        #if $quant_type.qtype == "reads":
+            #if $quant_type.writeMappings:
+                && samtools view -S -b ./output/samout.sam > ./output/bamout.bam
+            #end if
+        #end if
+        #if $quant_type.qtype == "alignment":
+            #if $quant_type.sampleOut:
+                && samtools sort -@ 4 -o ./output/postSample_sorted.bam ./output/postSample.bam
+            #end if
+        #end if
+        ]]>
+    </command>
+    <inputs>
+        <conditional name="quant_type">
+            <param name="qtype" type="select" label="Select salmon quantification mode:">
+                <option value="reads" selected="True">Reads</option>
+                <option value="alignment">Alignment</option>
+            </param>
+            <when value="reads">
+                <expand macro="index"/>
+                <expand macro="reads"/>
+            </when>
+            <when value="alignment">
+                <expand macro="align"/>
+            </when>
+        </conditional>
+        <expand macro="quantboth"/>
+    </inputs>
+    <outputs>
+        <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
+        <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
+            <filter>geneMap</filter>
+        </data>
+        <data name="output_bam" format="bam" from_work_dir="output/bamout.bam" label="${tool.name} on ${on_string} (BAM format)">
+            <filter>quant_type['qtype'] == "reads" and quant_type['writeMappings']</filter>
+        </data>
+        <data name="postSample" format="bam" from_work_dir="./output/postSample_sorted.bam" label="Sampled input alignments on ${on_string}(BAM format)">
+            <filter>quant_type['qtype'] == "alignment" and quant_type['sampleOut']</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <conditional name="quant_type">
+                <param name="qtype" value="reads"/>
+                <conditional name="refTranscriptSource">
+                    <param name="TranscriptSource" value="history"/>
+                    <section name="s_index">
+                        <param name="fasta" value="transcripts.fasta"/>
+                    </section>
+                </conditional>
+                <section name="input">
+                    <param name="single_or_paired.single_or_paired_opts" value="paired" />
+                    <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" />
+                    <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" />
+                    <param name="single_or_paired.strandedness" value="U"/>
+                </section>
+                <param name="writeMappings" value="true"/>
+            </conditional>
+            <output name="output_quant" ftype="tabular">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="NM_001168316" />
+                    <has_text text="NM_174914" />
+                    <has_text text="NM_018953" />
+                    <has_text text="NR_003084" />
+                    <has_text text="NM_017410" />
+                    <has_text text="NM_153693" />
+                    <has_text text="NR_031764" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="quant_type">
+                <param name="qtype" value="reads"/>
+                <conditional name="refTranscriptSource">
+                    <param name="TranscriptSource" value="history"/>
+                    <section name="s_index">
+                        <param name="fasta" value="transcripts.fasta"/>
+                    </section>
+                </conditional>
+                <section name="input">
+                    <param name="single_or_paired.single_or_paired_opts" value="paired" />
+                    <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq.gz" />
+                    <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq.gz" />
+                    <param name="single_or_paired.strandedness" value="U"/>
+                </section>
+            </conditional>
+            <output name="output_quant" ftype="tabular">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="NM_001168316" />
+                    <has_text text="NM_174914" />
+                    <has_text text="NM_018953" />
+                    <has_text text="NR_003084" />
+                    <has_text text="NM_017410" />
+                    <has_text text="NM_153693" />
+                    <has_text text="NR_031764" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="quant_type">
+                <param name="qtype" value="reads"/>
+                <conditional name="refTranscriptSource">
+                    <param name="TranscriptSource" value="history"/>
+                    <section name="s_index">
+                        <param name="fasta" value="transcripts.fasta"/>
+                    </section>
+                </conditional>
+                <section name="input">
+                    <param name="single_or_paired.single_or_paired_opts" value="single" />
+                    <param name="single_or_paired.input_mate1" value="fastqs/reads_both.fastq.bz2" />
+                    <param name="single_or_paired.strandedness" value="U"/>
+                </section>
+            </conditional>
+            <output name="output_quant" ftype="tabular">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="NM_001168316" />
+                    <has_text text="NM_174914" />
+                    <has_text text="NM_018953" />
+                    <has_text text="NR_003084" />
+                    <has_text text="NM_017410" />
+                    <has_text text="NM_153693" />
+                    <has_text text="NR_031764" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="2">
+            <conditional name="quant_type">
+                <param name="qtype" value="alignment"/>
+                <param name="afile" value="salmonbam.bam"/>
+                <param name="transcript" value="transcripts.fasta"/>
+                <param name="sampleOut" value="--sampleOut"/>
+                <param name="sampleUnaligned" value="--sampleUnaligned"/>
+                <param name="noErrorModel" value="--noErrorModel"/>
+                <param name="numErrorBins" value="5"/>
+            </conditional>
+            <output name="postSample" ftype="bam" value="postSample.bam"/>
+            <assert_stderr>
+                <has_text text="Sampling alignments; outputting results to ./output/postSample.bam"/>
+            </assert_stderr>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="quant_type">
+                <param name="qtype" value="reads"/>
+                <conditional name="refTranscriptSource">
+                    <param name="TranscriptSource" value="history"/>
+                    <section name="s_index">
+                        <param name="fasta" value="transcripts.fasta"/>
+                    </section>
+                </conditional>
+                <section name="input">
+                    <param name="single_or_paired.single_or_paired_opts" value="paired" />
+                    <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" />
+                    <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" />
+                    <param name="single_or_paired.strandeness" value="U"/>
+                </section>
+                <param name="discardOrphansQuasi" value="-discardOrphansQuasi"/>
+                <conditional name="validmap">
+                    <param name="validateMappings" value="--validateMappings"/>
+                </conditional>
+                <param name="dovetail" value="--allowDovetail"/>
+                <param name="recoverOrphans" value="--recoverOrphans"/>
+            </conditional>
+            <output name="output_quant" ftype="tabular">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="NM_001168316" />
+                    <has_text text="NM_174914" />
+                    <has_text text="NM_018953" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="quant_type">
+                <param name="qtype" value="reads"/>
+                <conditional name="refTranscriptSource">
+                    <param name="TranscriptSource" value="history"/>
+                    <section name="s_index">
+                        <param name="fasta" value="transcripts.fasta"/>
+                    </section>
+                </conditional>
+                <section name="input">
+                    <param name="single_or_paired.single_or_paired_opts" value="paired" />
+                    <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" />
+                    <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" />
+                    <param name="single_or_paired.strandedness" value="U"/>
+                </section>
+            </conditional>
+            <param name="seqBias" value="--seqBias"/>
+            <param name="gcBias" value="--gcBias"/>
+            <section name="adv">
+                <param name="dumpEq" value="--dumpEq"/>
+                <param name="minAssignedFrags" value="10"/>
+                <param name="noLengthCorrection"/>
+                <param name="initUniform" value="--initUniform"/>
+                <param name="useEM" value="--useEM"/>
+                <param name="noGammaDraw" value="--noGammaDraw"/>
+            </section>
+            <output name="output_quant" ftype="tabular">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="quant_type">
+                <param name="qtype" value="reads"/>
+                <conditional name="refTranscriptSource">
+                    <param name="TranscriptSource" value="indexed"/>
+                    <param name="index" value="hg19_transcript_subset" />
+                </conditional>
+                <section name="input">
+                    <conditional name="single_or_paired">
+                        <param name="single_or_paired_opts" value="paired" />
+                        <param name="input_mate1" value="fastqs/reads_1.fastq" />
+                        <param name="input_mate2" value="fastqs/reads_2.fastq" />
+                        <param name="strandedness" value="U"/>
+                    </conditional>
+                </section>
+            </conditional>
+            <output name="output_quant" ftype="tabular">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="NM_001168316" />
+                    <has_text text="NM_174914" />
+                    <has_text text="NM_018953" />
+                    <has_text text="NR_003084" />
+                    <has_text text="NM_017410" />
+                    <has_text text="NM_153693" />
+                    <has_text text="NR_031764" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        @salmonhelp@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>