Mercurial > repos > ebi-gxa > fastq_filter_n
annotate fastq_filter_n.xml @ 0:df87d29fac7f draft default tip
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
author | ebi-gxa |
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date | Tue, 15 Feb 2022 16:38:56 +0000 |
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df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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1 <tool id="fastq_filter_n" name="FASTQ filterer" profile="18.01" version="0.25.1+galaxy0"> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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2 <description>Discards reads with more than x% of uncalled bases (N)</description> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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3 <requirements> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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4 <requirement type="package" version="0.25.1">fastq_utils</requirement> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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5 </requirements> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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6 <command detect_errors="exit_code"><![CDATA[ |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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7 fastq_filter_n -n '$threshold' '$file' > $outfile |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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8 ]]></command> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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9 <inputs> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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10 <param name="file" label="Input file" type="data" format="fastqsanger.gz" optional="false" help="Fastq (optional gzipped) file name"/> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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11 <param name="threshold" label="Filter threshold" argument="-n" optional="true" value="0" type="integer" min="0" max="100" help="[0-100] Maximum percentage of uncalled bases in a read. Default is 0."/> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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12 </inputs> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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13 <outputs> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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14 <data label="${tool.name} on ${on_string}: Output file" name="outfile" format="fastqsanger.gz" /> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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15 </outputs> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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16 <tests> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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17 <test> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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18 <param name="file" value="test_21_2.fastq.gz"/> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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19 <param name="threshold" value="5"/> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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20 <output name="outfile" md5="019ce04559162b973e13a514a5c01595"/> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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21 </test> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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22 </tests> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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23 <help><![CDATA[ |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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24 ============================================================ |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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25 FASTQ filterer (fastq_filter_n) |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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26 ============================================================ |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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27 |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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28 Outputs a gzipped fastq file where reads with more than the |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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29 maximum number of allowed uncalled bases are not included. |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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30 |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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31 Threshold is the maximum percentage (ranging from 0 to 100) |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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32 of uncalled bases that a read can have. Default value is 0, |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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33 which means that a read with a single N would be discarded. |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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34 |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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35 ]]></help> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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36 <citations> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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37 <citation type="bibtex"><![CDATA[ |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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38 @ARTICLE{Fonseca2017, |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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39 author = {Fonseca, N.}, |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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40 title = {fastq_utils}, |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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41 year = {2017}, |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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42 publisher = {GitHub}, |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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43 journal = {GitHub repository}, |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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44 howpublished = {\url{https://github.com/nunofonseca/fastq_utils}}, |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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45 commit = {c6cf3f954c5286e62fbe36bb9ffecd89d7823b07} |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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46 }]]></citation> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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47 </citations> |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
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48 </tool> |