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Allow non-coordinate-sorted bam input to eXpress #581

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Allow non-coordinate-sorted bam input to eXpress #581

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8b4620d
Allow non-coordinate-sorted bam input to eXpress
Dec 22, 2020
e55ec43
Merge remote-tracking branch 'upstream/master'
Dec 29, 2020
352e463
Remove (sorted) bam input for eXpress
Dec 29, 2020
b5b7756
Remove redundant dependencies file for eXpress
Dec 29, 2020
0860a87
Upgrade eXpress to version 1.5.1
Dec 29, 2020
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6 changes: 3 additions & 3 deletions tools/express/express_wrapper.xml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
<tool id="express" name="eXpress" version="1.1.1">
<tool id="express" name="eXpress" version="1.5.1">
<description>Quantify the abundances of a set of target sequences from sampled subsequences</description>
<requirements>
<requirement type="package" version="1.1.1">eXpress</requirement>
<requirement type="package" version="1.5.1">eXpress</requirement>
</requirements>
<command>
express --no-update-check
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Suggested change
express --no-update-check
#if $bamOrSamFile.ext == "qname_sorted.bam"
ln -s `$bamOrSamFile` hits.sorted
#else
samtools sort -n '$bamOrSamFile' hits.sorted
#end if
express --no-update-check

Plus: replace $bamOrSamFile on the last line of the command block with hits.sorted (btw. all input files need to be single quoted).

Maybe in the else branch one could check with samtools view -H ... | grep -q "@HD\t.*\tSO:unsorted" if the sam / bam file is sorted before calling sort again.

Expand All @@ -25,7 +25,7 @@
</command>
<inputs>
<param format="fasta" name="multiFasta" type="data" label="A set of target references (annotation) in multi-FASTA format" help="The multi-FASTA file can also be a fasta file." />
<param format="sam,bam" name="bamOrSamFile" type="data" label="Alignments in the BAM or SAM format" help="The set of aligned reads." />
<param format="sam,unsorted.bam,qname_sorted.bam" name="bamOrSamFile" type="data" label="Alignments in the BAM or SAM format" help="The set of aligned reads." />
<conditional name="additional_params">
<param name="use_additional" type="select" label="Use Additional Parameters?">
<option value="no">No</option>
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6 changes: 0 additions & 6 deletions tools/express/tool_dependencies.xml
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