Mercurial > repos > bgruening > salmon

annotate salmonquant.xml @ 18:c6c81a918ae1 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
author bgruening
date Thu, 22 Jul 2021 14:02:44 +0000
parents 818b16dd05a1
children accd772edf70
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c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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1 <tool id="salmon" name="Salmon quant" version="@VERSION@+@GALAXY_VERSION@" profile="@PROFILE_VERSION@">
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2 <description>Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="aggressive"><![CDATA[
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8 #if $quant_type.qtype == "reads":
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9 @indexing@
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10 @salreads@
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11 #else:
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12 @salalign@
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13 #end if
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14 @salquant@
15
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15 #if $quant_type.qtype == "reads" and $quant_type.writeMappings:
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16 && @bam_sort@ ./output/samout.sam
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17 #end if
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18 #if $quant_type.qtype == "alignment" and $quant_type.sampleOut:
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19 && @bam_sort@ ./output/postSample.bam
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20 #end if
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21 ]]>
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22 </command>
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23 <inputs>
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24 <conditional name="quant_type">
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25 <param name="qtype" type="select" label="Select salmon quantification mode:">
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26 <option value="reads" selected="True">Reads</option>
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27 <option value="alignment">Alignment</option>
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28 </param>
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29 <when value="reads">
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30 <expand macro="index"/>
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31 <expand macro="reads"/>
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32 </when>
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33 <when value="alignment">
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34 <expand macro="align"/>
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35 </when>
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36 </conditional>
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37 <expand macro="quantboth"/>
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38 </inputs>
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39 <outputs>
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40 <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
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41 <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
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42 <filter>geneMap</filter>
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43 </data>
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44 <data name="output_bam" format="bam" from_work_dir="output/bamout.bam" label="${tool.name} on ${on_string} (BAM format)">
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45 <filter>quant_type['qtype'] == "reads" and quant_type['writeMappings']</filter>
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46 </data>
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47 <data name="postSample" format="bam" from_work_dir="output/bamout.bam" label="Sampled input alignments on ${on_string}(BAM format)">
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48 <filter>quant_type['qtype'] == "alignment" and quant_type['sampleOut']</filter>
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49 </data>
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50 </outputs>
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51 <tests>
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52 <test expect_num_outputs="2">
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53 <conditional name="quant_type">
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54 <param name="qtype" value="reads"/>
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55 <conditional name="refTranscriptSource">
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56 <param name="TranscriptSource" value="history"/>
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57 <section name="s_index">
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58 <param name="fasta" value="transcripts.fasta"/>
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59 </section>
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60 </conditional>
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61 <section name="input">
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62 <conditional name="single_or_paired">
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63 <param name="single_or_paired_opts" value="paired" />
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64 <param name="input_mate1" value="fastqs/reads_1.fastq" />
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65 <param name="input_mate2" value="fastqs/reads_2.fastq" />
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66 <conditional name="libtype">
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67 <param name="strandedness" value="U"/>
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68 </conditional>
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69 </conditional>
12
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70 </section>
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71 <param name="writeMappings" value="true"/>
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72 </conditional>
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73 <output name="output_quant" ftype="tabular">
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74 <assert_contents>
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75 <has_text text="EffectiveLength" />
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76 <has_text text="TPM" />
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77 <has_text text="NM_001168316" />
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78 <has_text text="NM_174914" />
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79 <has_text text="NM_018953" />
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80 <has_text text="NR_003084" />
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81 <has_text text="NM_017410" />
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82 <has_text text="NM_153693" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
83 <has_text text="NR_031764" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
84 <has_n_columns n="5" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
85 </assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
86 </output>
18
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
87 <assert_command>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
88 <has_text text="--libType IU"/>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
89 </assert_command>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
90 </test>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
91 <test expect_num_outputs="2">
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
92 <conditional name="quant_type">
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
93 <param name="qtype" value="reads"/>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
94 <conditional name="refTranscriptSource">
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
95 <param name="TranscriptSource" value="history"/>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
96 <section name="s_index">
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
97 <param name="fasta" value="transcripts.fasta"/>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
98 </section>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
99 </conditional>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
100 <section name="input">
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
101 <param name="single_or_paired.single_or_paired_opts" value="paired" />
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
102 <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" />
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
103 <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" />
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
104 </section>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
105 <param name="writeMappings" value="true"/>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
106 </conditional>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
107 <output name="output_quant" ftype="tabular">
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
108 <assert_contents>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
109 <has_text text="EffectiveLength" />
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
110 <has_text text="TPM" />
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
111 <has_text text="NM_001168316" />
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
112 <has_text text="NM_174914" />
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
113 <has_text text="NM_018953" />
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
114 <has_text text="NR_003084" />
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
115 <has_text text="NM_017410" />
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
116 <has_text text="NM_153693" />
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
117 <has_text text="NR_031764" />
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
118 <has_n_columns n="5" />
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
119 </assert_contents>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
120 </output>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
121 <assert_command>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
122 <has_text text="--libType A"/>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
123 </assert_command>
12
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
124 </test>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
125 <test expect_num_outputs="1">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
126 <conditional name="quant_type">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
127 <param name="qtype" value="reads"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
128 <conditional name="refTranscriptSource">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
129 <param name="TranscriptSource" value="history"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
130 <section name="s_index">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
131 <param name="fasta" value="transcripts.fasta"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
132 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
133 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
134 <section name="input">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
135 <param name="single_or_paired.single_or_paired_opts" value="paired" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
136 <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq.gz" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
137 <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq.gz" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
138 <param name="single_or_paired.strandedness" value="U"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
139 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
140 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
141 <output name="output_quant" ftype="tabular">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
142 <assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
143 <has_text text="EffectiveLength" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
144 <has_text text="TPM" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
145 <has_text text="NM_001168316" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
146 <has_text text="NM_174914" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
147 <has_text text="NM_018953" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
148 <has_text text="NR_003084" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
149 <has_text text="NM_017410" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
150 <has_text text="NM_153693" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
151 <has_text text="NR_031764" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
152 <has_n_columns n="5" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
153 </assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
154 </output>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
155 </test>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
156 <test expect_num_outputs="1">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
157 <conditional name="quant_type">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
158 <param name="qtype" value="reads"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
159 <conditional name="refTranscriptSource">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
160 <param name="TranscriptSource" value="history"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
161 <section name="s_index">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
162 <param name="fasta" value="transcripts.fasta"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
163 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
164 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
165 <section name="input">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
166 <param name="single_or_paired.single_or_paired_opts" value="single" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
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167 <param name="single_or_paired.input_mate1" value="fastqs/reads_both.fastq.bz2" />
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168 <param name="single_or_paired.strandedness" value="U"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
169 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
170 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
171 <output name="output_quant" ftype="tabular">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
172 <assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
173 <has_text text="EffectiveLength" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
174 <has_text text="TPM" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
175 <has_text text="NM_001168316" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
176 <has_text text="NM_174914" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
177 <has_text text="NM_018953" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
178 <has_text text="NR_003084" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
179 <has_text text="NM_017410" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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180 <has_text text="NM_153693" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
181 <has_text text="NR_031764" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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182 <has_n_columns n="5" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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183 </assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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184 </output>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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185 </test>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
186 <test expect_num_outputs="2">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
187 <conditional name="quant_type">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
188 <param name="qtype" value="alignment"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
189 <param name="afile" value="salmonbam.bam"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
190 <param name="transcript" value="transcripts.fasta"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
191 <param name="sampleOut" value="--sampleOut"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
192 <param name="sampleUnaligned" value="--sampleUnaligned"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
193 <param name="noErrorModel" value="--noErrorModel"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
194 <param name="numErrorBins" value="5"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
195 </conditional>
18
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
196 <!-- bam output uses non-deterministic sampling, so can only use compare="sim_size" -->
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
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diff changeset
197 <output name="postSample" ftype="bam" value="postSample.bam" compare="sim_size" delta="20000"/>
12
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
198 <assert_stderr>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
199 <has_text text="Sampling alignments; outputting results to ./output/postSample.bam"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
200 </assert_stderr>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
201 </test>
18
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
202 <test expect_num_outputs="2">
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
203 <conditional name="quant_type">
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
204 <param name="qtype" value="alignment"/>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
205 <param name="afile" value="salmonbam.bam"/>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
206 <param name="ont" value="true" />
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
207 <param name="transcript" value="transcripts.fasta"/>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
208 <param name="sampleOut" value="--sampleOut"/>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
209 <param name="sampleUnaligned" value="--sampleUnaligned"/>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
210 <param name="noErrorModel" value="--noErrorModel"/>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
211 <param name="numErrorBins" value="5"/>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
212 </conditional>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
213 <assert_stderr>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
214 <has_text text="Sampling alignments; outputting results to ./output/postSample.bam"/>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
215 </assert_stderr>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
216 <assert_command>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
217 <has_text text=" --ont "/>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
218 </assert_command>
c6c81a918ae1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 15
diff changeset
219 </test>
12
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
220 <test expect_num_outputs="1">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
221 <conditional name="quant_type">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
222 <param name="qtype" value="reads"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
223 <conditional name="refTranscriptSource">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
224 <param name="TranscriptSource" value="history"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
225 <section name="s_index">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
226 <param name="fasta" value="transcripts.fasta"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
227 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
228 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
229 <section name="input">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
230 <param name="single_or_paired.single_or_paired_opts" value="paired" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
231 <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
232 <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
233 <param name="single_or_paired.strandeness" value="U"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
234 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
235 <param name="discardOrphansQuasi" value="-discardOrphansQuasi"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
236 <conditional name="validmap">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
237 <param name="validateMappings" value="--validateMappings"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
238 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
239 <param name="dovetail" value="--allowDovetail"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
240 <param name="recoverOrphans" value="--recoverOrphans"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
241 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
242 <output name="output_quant" ftype="tabular">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
243 <assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
244 <has_text text="EffectiveLength" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
245 <has_text text="TPM" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
246 <has_text text="NM_001168316" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
247 <has_text text="NM_174914" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
248 <has_text text="NM_018953" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
249 <has_n_columns n="5" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
250 </assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
251 </output>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
252 </test>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
253 <test expect_num_outputs="1">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
254 <conditional name="quant_type">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
255 <param name="qtype" value="reads"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
256 <conditional name="refTranscriptSource">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
257 <param name="TranscriptSource" value="history"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
258 <section name="s_index">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
259 <param name="fasta" value="transcripts.fasta"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
260 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
261 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
262 <section name="input">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
263 <param name="single_or_paired.single_or_paired_opts" value="paired" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
264 <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
265 <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
266 <param name="single_or_paired.strandedness" value="U"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
267 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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268 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
269 <param name="seqBias" value="--seqBias"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
270 <param name="gcBias" value="--gcBias"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
271 <section name="adv">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
272 <param name="dumpEq" value="--dumpEq"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
273 <param name="minAssignedFrags" value="10"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
274 <param name="noLengthCorrection"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
275 <param name="initUniform" value="--initUniform"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
276 <param name="useEM" value="--useEM"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
277 <param name="noGammaDraw" value="--noGammaDraw"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
278 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
279 <output name="output_quant" ftype="tabular">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
280 <assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
281 <has_text text="EffectiveLength" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
282 <has_text text="TPM" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
283 <has_n_columns n="5" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
284 </assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
285 </output>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
286 </test>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
287 <test expect_num_outputs="1">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
288 <conditional name="quant_type">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
289 <param name="qtype" value="reads"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
290 <conditional name="refTranscriptSource">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
291 <param name="TranscriptSource" value="indexed"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
292 <param name="index" value="hg19_transcript_subset" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
293 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
294 <section name="input">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
295 <conditional name="single_or_paired">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
296 <param name="single_or_paired_opts" value="paired" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
297 <param name="input_mate1" value="fastqs/reads_1.fastq" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
298 <param name="input_mate2" value="fastqs/reads_2.fastq" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
299 <param name="strandedness" value="U"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
300 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
301 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
302 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
303 <output name="output_quant" ftype="tabular">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
304 <assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
305 <has_text text="EffectiveLength" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
306 <has_text text="TPM" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
307 <has_text text="NM_001168316" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
308 <has_text text="NM_174914" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
309 <has_text text="NM_018953" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
310 <has_text text="NR_003084" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
311 <has_text text="NM_017410" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
312 <has_text text="NM_153693" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
313 <has_text text="NR_031764" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
314 <has_n_columns n="5" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
315 </assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
316 </output>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
317 </test>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
318 </tests>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
319 <help><![CDATA[
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
320 @salmonhelp@
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
321 ]]></help>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
322 <expand macro="citations"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
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diff changeset
323 </tool>