Mercurial > repos > q2d2 > qiime2_core__tools__import

changeset 1:5d9a36073ed6 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 23:02:20 +0000
parents 1370f8d6e95b
children 18c6b2b6740f
files qiime2_core__tools__import.xml
diffstat 1 files changed, 215 insertions(+), 53 deletions(-) [+]
line wrap: on
line diff
--- a/qiime2_core__tools__import.xml	Mon Aug 29 20:36:58 2022 +0000
+++ b/qiime2_core__tools__import.xml	Fri Jan 13 23:02:20 2023 +0000
@@ -1,21 +1,21 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2022, QIIME 2 development team.
+Copyright (c) 2023, QIIME 2 development team.
 
 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2022.8.1)
+    q2galaxy (version: 2022.11.1)
 for:
-    qiime2 (version: 2022.8.1)
+    qiime2 (version: 2022.11.1)
 -->
-<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2022.8.1+dist.h91e3be72.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2022.11.1+dist.h2bda5906.2" profile="22.05" license="BSD-3-Clause">
     <description>Import data into a QIIME 2 artifact</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2022.8</container>
+        <container type="docker">quay.io/qiime2/core:2022.11</container>
     </requirements>
-    <command>q2galaxy run tools import '$inputs'</command>
+    <command detect_errors="exit_code">q2galaxy run tools import '$inputs'</command>
     <configfiles>
         <configfile name="inputs">&lt;%
 # This is an exercise in cheating the Cheetah
@@ -69,6 +69,7 @@
                 <option value="FeatureData__ob__AlignedRNASequence__cb__">FeatureData[AlignedRNASequence]</option>
                 <option value="FeatureData__ob__AlignedSequence__cb__">FeatureData[AlignedSequence]</option>
                 <option value="FeatureData__ob__BLAST6__cb__">FeatureData[BLAST6]</option>
+                <option value="FeatureData__ob__DifferentialAbundance__cb__">FeatureData[DifferentialAbundance]</option>
                 <option value="FeatureData__ob__Differential__cb__">FeatureData[Differential]</option>
                 <option value="FeatureData__ob__Importance__cb__">FeatureData[Importance]</option>
                 <option value="FeatureData__ob__PairedEndRNASequence__cb__">FeatureData[PairedEndRNASequence]</option>
@@ -279,6 +280,7 @@
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
                         <option value="AlignedRNAFASTAFormat" selected="true">Aligned RNAFASTA Format</option>
+                        <option value="MixedCaseAlignedRNAFASTAFormat" selected="false">Mixed Case Aligned RNAFASTA Format</option>
                     </param>
                     <when value="AlignedRNAFASTAFormat">
                         <section name="import" expanded="true" title="Import">
@@ -286,12 +288,19 @@
                             <param name="data" type="data" format="data" help="This data should be formatted as a AlignedRNAFASTAFormat. See the documentation below for more information."/>
                         </section>
                     </when>
+                    <when value="MixedCaseAlignedRNAFASTAFormat">
+                        <section name="import" expanded="true" title="Import">
+                            <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a MixedCaseAlignedRNAFASTAFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
                 </conditional>
             </when>
             <when value="FeatureData__ob__AlignedSequence__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
                         <option value="AlignedDNAFASTAFormat" selected="true">Aligned DNAFASTA Format</option>
+                        <option value="MixedCaseAlignedDNAFASTAFormat" selected="false">Mixed Case Aligned DNAFASTA Format</option>
                     </param>
                     <when value="AlignedDNAFASTAFormat">
                         <section name="import" expanded="true" title="Import">
@@ -299,6 +308,12 @@
                             <param name="data" type="data" format="data" help="This data should be formatted as a AlignedDNAFASTAFormat. See the documentation below for more information."/>
                         </section>
                     </when>
+                    <when value="MixedCaseAlignedDNAFASTAFormat">
+                        <section name="import" expanded="true" title="Import">
+                            <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a MixedCaseAlignedDNAFASTAFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
                 </conditional>
             </when>
             <when value="FeatureData__ob__BLAST6__cb__">
@@ -314,6 +329,48 @@
                     </when>
                 </conditional>
             </when>
+            <when value="FeatureData__ob__DifferentialAbundance__cb__">
+                <conditional name="__q2galaxy__GUI__cond__format__">
+                    <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="DataLoafPackageDirFmt" selected="true">Data Loaf Package Directory Format</option>
+                    </param>
+                    <when value="DataLoafPackageDirFmt">
+                        <section name="import_data_slices" expanded="true" title="Import data_slices">
+                            <conditional name="__q2galaxy__GUI__cond__data_slices__">
+                                <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism">
+                                    <option value="collection" selected="true">Use collection to import</option>
+                                    <option value="individual">Associate individual files</option>
+                                </param>
+                                <when value="collection">
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FrictionlessCSVFileFormat. See the documentation below for more information. Elements must match regex: .+\.csv"/>
+                                    <conditional name="__q2galaxy__GUI__cond__add_ext__">
+                                        <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
+                                            <option value="no">No, use element identifiers as is</option>
+                                            <option value="yes">Yes, append an extension</option>
+                                        </param>
+                                        <when value="yes">
+                                            <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
+                                        </when>
+                                        <when value="no"/>
+                                    </conditional>
+                                </when>
+                                <when value="individual">
+                                    <repeat name="elements" min="1" title="Add Elements">
+                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.csv">
+                                            <validator type="regex" message="This filename doesn't match the regex.">.+\.csv</validator>
+                                        </param>
+                                        <param name="data" type="data" format="data" help="This data should be formatted as a FrictionlessCSVFileFormat. See the documentation below for more information."/>
+                                    </repeat>
+                                </when>
+                            </conditional>
+                        </section>
+                        <section name="import_nutrition_facts" expanded="true" title="Import nutrition_facts">
+                            <param name="name" type="text" value="datapackage.json" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a DataPackageSchemaFileFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
+                </conditional>
+            </when>
             <when value="FeatureData__ob__Differential__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
@@ -390,8 +447,15 @@
             <when value="FeatureData__ob__RNASequence__cb__">
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
+                        <option value="MixedCaseRNAFASTAFormat" selected="false">Mixed Case RNAFASTA Format</option>
                         <option value="RNAFASTAFormat" selected="true">RNAFASTA Format</option>
                     </param>
+                    <when value="MixedCaseRNAFASTAFormat">
+                        <section name="import" expanded="true" title="Import">
+                            <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a MixedCaseRNAFASTAFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
                     <when value="RNAFASTAFormat">
                         <section name="import" expanded="true" title="Import">
                             <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
@@ -404,6 +468,7 @@
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
                         <option value="DNAFASTAFormat" selected="true">DNAFASTA Format</option>
+                        <option value="MixedCaseDNAFASTAFormat" selected="false">Mixed Case DNAFASTA Format</option>
                     </param>
                     <when value="DNAFASTAFormat">
                         <section name="import" expanded="true" title="Import">
@@ -411,6 +476,12 @@
                             <param name="data" type="data" format="data" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information."/>
                         </section>
                     </when>
+                    <when value="MixedCaseDNAFASTAFormat">
+                        <section name="import" expanded="true" title="Import">
+                            <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a MixedCaseDNAFASTAFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
                 </conditional>
             </when>
             <when value="FeatureData__ob__Taxonomy__cb__">
@@ -614,6 +685,7 @@
                 <conditional name="__q2galaxy__GUI__cond__format__">
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
                         <option value="FastqGzFormat" selected="true">Fastq Gz Format</option>
+                        <option value="MultiplexedFastaQualDirFmt" selected="false">Multiplexed Fasta Qual Directory Format</option>
                     </param>
                     <when value="FastqGzFormat">
                         <section name="import" expanded="true" title="Import">
@@ -621,6 +693,16 @@
                             <param name="data" type="data" format="data" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information."/>
                         </section>
                     </when>
+                    <when value="MultiplexedFastaQualDirFmt">
+                        <section name="import_sequences" expanded="true" title="Import sequences">
+                            <param name="name" type="text" value="reads.fasta" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information."/>
+                        </section>
+                        <section name="import_quality" expanded="true" title="Import quality">
+                            <param name="name" type="text" value="reads.qual" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/>
+                            <param name="data" type="data" format="data" help="This data should be formatted as a QualFormat. See the documentation below for more information."/>
+                        </section>
+                    </when>
                 </conditional>
             </when>
             <when value="PCoAResults">
@@ -812,6 +894,7 @@
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
                         <option value="CasavaOneEightLanelessPerSampleDirFmt" selected="false">Casava One Eight Laneless Per Sample Directory Format</option>
                         <option value="CasavaOneEightSingleLanePerSampleDirFmt" selected="false">Casava One Eight Single Lane Per Sample Directory Format</option>
+                        <option value="SampleIdIndexedSingleEndPerSampleDirFmt" selected="false">Sample Id Indexed Single End Per Sample Directory Format</option>
                         <option value="SingleEndFastqManifestPhred33" selected="false">Single End Fastq Manifest Phred33</option>
                         <option value="SingleEndFastqManifestPhred33V2" selected="false">Single End Fastq Manifest Phred33V2</option>
                         <option value="SingleEndFastqManifestPhred64" selected="false">Single End Fastq Manifest Phred64</option>
@@ -881,6 +964,37 @@
                             </conditional>
                         </section>
                     </when>
+                    <when value="SampleIdIndexedSingleEndPerSampleDirFmt">
+                        <section name="import_sequences" expanded="true" title="Import sequences">
+                            <conditional name="__q2galaxy__GUI__cond__sequences__">
+                                <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism">
+                                    <option value="collection" selected="true">Use collection to import</option>
+                                    <option value="individual">Associate individual files</option>
+                                </param>
+                                <when value="collection">
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+\.fastq\.gz"/>
+                                    <conditional name="__q2galaxy__GUI__cond__add_ext__">
+                                        <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
+                                            <option value="no">No, use element identifiers as is</option>
+                                            <option value="yes">Yes, append an extension</option>
+                                        </param>
+                                        <when value="yes">
+                                            <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
+                                        </when>
+                                        <when value="no"/>
+                                    </conditional>
+                                </when>
+                                <when value="individual">
+                                    <repeat name="elements" min="1" title="Add Elements">
+                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.fastq\.gz">
+                                            <validator type="regex" message="This filename doesn't match the regex.">.+\.fastq\.gz</validator>
+                                        </param>
+                                        <param name="data" type="data" format="data" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information."/>
+                                    </repeat>
+                                </when>
+                            </conditional>
+                        </section>
+                    </when>
                     <when value="SingleEndFastqManifestPhred33">
                         <section name="import" expanded="true" title="Import">
                             <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
@@ -1154,6 +1268,7 @@
                     <param name="format" type="select" label="QIIME 2 file format to import from:">
                         <option value="CasavaOneEightLanelessPerSampleDirFmt" selected="false">Casava One Eight Laneless Per Sample Directory Format</option>
                         <option value="CasavaOneEightSingleLanePerSampleDirFmt" selected="false">Casava One Eight Single Lane Per Sample Directory Format</option>
+                        <option value="SampleIdIndexedSingleEndPerSampleDirFmt" selected="false">Sample Id Indexed Single End Per Sample Directory Format</option>
                         <option value="SingleEndFastqManifestPhred33" selected="false">Single End Fastq Manifest Phred33</option>
                         <option value="SingleEndFastqManifestPhred33V2" selected="false">Single End Fastq Manifest Phred33V2</option>
                         <option value="SingleEndFastqManifestPhred64" selected="false">Single End Fastq Manifest Phred64</option>
@@ -1223,6 +1338,37 @@
                             </conditional>
                         </section>
                     </when>
+                    <when value="SampleIdIndexedSingleEndPerSampleDirFmt">
+                        <section name="import_sequences" expanded="true" title="Import sequences">
+                            <conditional name="__q2galaxy__GUI__cond__sequences__">
+                                <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism">
+                                    <option value="collection" selected="true">Use collection to import</option>
+                                    <option value="individual">Associate individual files</option>
+                                </param>
+                                <when value="collection">
+                                    <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+\.fastq\.gz"/>
+                                    <conditional name="__q2galaxy__GUI__cond__add_ext__">
+                                        <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
+                                            <option value="no">No, use element identifiers as is</option>
+                                            <option value="yes">Yes, append an extension</option>
+                                        </param>
+                                        <when value="yes">
+                                            <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
+                                        </when>
+                                        <when value="no"/>
+                                    </conditional>
+                                </when>
+                                <when value="individual">
+                                    <repeat name="elements" min="1" title="Add Elements">
+                                        <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.fastq\.gz">
+                                            <validator type="regex" message="This filename doesn't match the regex.">.+\.fastq\.gz</validator>
+                                        </param>
+                                        <param name="data" type="data" format="data" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information."/>
+                                    </repeat>
+                                </when>
+                            </conditional>
+                        </section>
+                    </when>
                     <when value="SingleEndFastqManifestPhred33">
                         <section name="import" expanded="true" title="Import">
                             <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
@@ -1514,12 +1660,15 @@
 --------
 These formats have documentation available.
 
-HeaderlessTSVTaxonomyFormat
-***************************
-Format for a 2+ column TSV file without a header.
+SampleIdIndexedSingleEndPerSampleDirFmt
+***************************************
+Single-end reads in fastq.gz files where base filename is the sample id
 
-This format supports comment lines starting with #, and blank lines.
-
+    The full file name, minus the extension (`.fastq.gz`) is the sample id.
+    For example, the sample id for the file:
+     * `sample-1.fastq.gz` is `sample-1`
+     * `xyz.fastq.gz` is `xyz`
+     * `sample-42_S1_L001_R1_001.fastq.gz` is `sample-42_S1_L001_R1_001`
 
 TSVTaxonomyFormat
 *****************
@@ -1570,6 +1719,13 @@
 - Each sequence must be DNA and cannot be empty.
 
 
+HeaderlessTSVTaxonomyFormat
+***************************
+Format for a 2+ column TSV file without a header.
+
+This format supports comment lines starting with #, and blank lines.
+
+
 FastqGzFormat
 *************
 
@@ -1578,56 +1734,62 @@
 
 Additional formats without documentation:
 *****************************************
- - PairedEndFastqManifestPhred64
- - SingleEndFastqManifestPhred64
- - NewickFormat
- - SeppReferenceDirFmt
- - PairedRNASequencesDirectoryFormat
- - EMPPairedEndDirFmt
- - ArtificialGroupingFormat
- - BLAST6Format
- - CasavaOneEightLanelessPerSampleDirFmt
- - ProbabilitiesFormat
- - PlacementsFormat
- - DADA2StatsFormat
- - SampleEstimatorDirFmt
- - ImportanceFormat
- - AlignedProteinFASTAFormat
- - SingleLanePerSampleSingleEndFastqDirFmt
- - BIOMV210Format
- - PairedEndFastqManifestPhred33V2
- - CasavaOneEightSingleLanePerSampleDirFmt
- - ProteinFASTAFormat
- - SingleEndFastqManifestPhred64V2
- - Bowtie2IndexDirFmt
- - DifferentialFormat
- - UchimeStatsFmt
+ - MixedCaseAlignedDNAFASTAFormat
  - DeblurStatsFmt
+ - DADA2StatsFormat
+ - PairedEndFastqManifestPhred64
+ - BIOMV210Format
+ - AlignedDNAFASTAFormat
+ - DataLoafPackageDirFmt
+ - SingleEndFastqManifestPhred64
+ - PairedDNASequencesDirectoryFormat
+ - BLAST6Format
+ - EMPPairedEndDirFmt
+ - PlacementsFormat
+ - AlignedProteinFASTAFormat
+ - MixedCaseRNAFASTAFormat
+ - FirstDifferencesFormat
+ - CasavaOneEightLanelessPerSampleDirFmt
+ - Bowtie2IndexDirFmt
+ - EMPSingleEndCasavaDirFmt
+ - ProcrustesStatisticsFmt
+ - ProteinFASTAFormat
+ - RNAFASTAFormat
+ - SingleLanePerSampleSingleEndFastqDirFmt
+ - PairedEndFastqManifestPhred33V2
+ - OrdinationFormat
+ - MixedCaseDNAFASTAFormat
+ - TaxonomicClassiferTemporaryPickleDirFmt
+ - ArtificialGroupingFormat
+ - BIOMV100Format
+ - CasavaOneEightSingleLanePerSampleDirFmt
+ - ErrorCorrectionDetailsFmt
+ - ImportanceFormat
+ - SingleEndFastqManifestPhred33V2
+ - DNAFASTAFormat
+ - MultiplexedFastaQualDirFmt
+ - PredictionsFormat
+ - MultiplexedPairedEndBarcodeInSequenceDirFmt
  - PairedEndFastqManifestPhred33
- - AlignedRNAFASTAFormat
+ - AlphaDiversityFormat
+ - ProbabilitiesFormat
  - EMPSingleEndDirFmt
+ - PairedRNASequencesDirectoryFormat
  - SingleEndFastqManifestPhred33
- - AlignedDNAFASTAFormat
+ - UchimeStatsFmt
  - EMPPairedEndCasavaDirFmt
- - ProcrustesStatisticsFmt
- - FirstDifferencesFormat
- - BIOMV100Format
- - PairedDNASequencesDirectoryFormat
- - MultiplexedPairedEndBarcodeInSequenceDirFmt
- - AlphaDiversityFormat
+ - NewickFormat
+ - SampleEstimatorDirFmt
+ - DifferentialFormat
  - LSMatFormat
- - BooleanSeriesFormat
- - OrdinationFormat
  - SingleLanePerSamplePairedEndFastqDirFmt
+ - QualityFilterStatsFmt
  - PairedEndFastqManifestPhred64V2
- - RNAFASTAFormat
- - TaxonomicClassiferTemporaryPickleDirFmt
- - PredictionsFormat
- - DNAFASTAFormat
- - QualityFilterStatsFmt
- - ErrorCorrectionDetailsFmt
- - EMPSingleEndCasavaDirFmt
- - SingleEndFastqManifestPhred33V2
+ - MixedCaseAlignedRNAFASTAFormat
+ - SingleEndFastqManifestPhred64V2
+ - AlignedRNAFASTAFormat
+ - BooleanSeriesFormat
+ - SeppReferenceDirFmt
 </help>
     <citations>
         <citation type="doi">10.1038/s41587-019-0209-9</citation>